Warning: Permanently added '169.63.181.217' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/6972644-fedora-39-s390x --chroot fedora-39-s390x Version: 0.70 PID: 7039 Logging PID: 7040 Task: {'appstream': False, 'background': True, 'build_id': 6972644, 'buildroot_pkgs': [], 'chroot': 'fedora-39-s390x', 'enable_net': False, 'fedora_review': False, 'git_hash': '6a1e15509098c91f653b329eac361b712a55cecb', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:2/seqan2', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'seqan2', 'package_version': '2.4.0-22', 'project_dirname': 'openblas-0.3.23:pr:2', 'project_name': 'openblas-0.3.23', 'project_owner': 'psimovec', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/openblas-0.3.23/fedora-39-s390x/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/rawhide/latest/$basearch/', 'id': 'http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch', 'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch'}], 'sandbox': 'psimovec/openblas-0.3.23--https://src.fedoraproject.org/user/jjames', 'source_json': {}, 'source_type': None, 'submitter': 'https://src.fedoraproject.org/user/jjames', 'tags': [], 'task_id': '6972644-fedora-39-s390x', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:2/seqan2 /var/lib/copr-rpmbuild/workspace/workdir-40ad8ut2/seqan2 --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:2/seqan2', '/var/lib/copr-rpmbuild/workspace/workdir-40ad8ut2/seqan2', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-40ad8ut2/seqan2'... Running: git checkout 6a1e15509098c91f653b329eac361b712a55cecb -- cmd: ['git', 'checkout', '6a1e15509098c91f653b329eac361b712a55cecb', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-40ad8ut2/seqan2 rc: 0 stdout: stderr: Note: switching to '6a1e15509098c91f653b329eac361b712a55cecb'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 6a1e155 automatic import of seqan2 Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-40ad8ut2/seqan2 rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading seqan-seqan-v2.4.0.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o seqan-seqan-v2.4.0.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/psimovec/openblas-0.3.23:pr:2/seqan2/seqan-seqan-v2.4.0.tar.gz/md5/d899821e295fed0a22e08099f40cbc17/seqan-seqan-v2.4.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 104M 100 104M 0 0 19.9M 0 0:00:05 0:00:05 --:--:-- 24.3M INFO: Reading stdout from command: md5sum seqan-seqan-v2.4.0.tar.gz /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-40ad8ut2/seqan2/seqan2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-40ad8ut2/seqan2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1706587007.973351 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.4 starting (python version = 3.11.3, NVR = mock-5.4-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-40ad8ut2/seqan2/seqan2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-40ad8ut2/seqan2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1706587007.973351 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-40ad8ut2/seqan2/seqan2.spec) Config(fedora-39-s390x) Start: clean chroot Finish: clean chroot Mock Version: 5.4 INFO: Mock Version: 5.4 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-s390x-bootstrap-1706587007.973351/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:39 INFO: Pulling image: registry.fedoraproject.org/fedora:39 INFO: Copy content of container registry.fedoraproject.org/fedora:39 to /var/lib/mock/fedora-39-s390x-bootstrap-1706587007.973351/root INFO: Checking that registry.fedoraproject.org/fedora:39 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:39 with podman image mount INFO: image registry.fedoraproject.org/fedora:39 as /var/lib/containers/storage/overlay/8762d4e942255ae5f22c1ca5cdcbea9118d53523b90ef15d705fc17a7574e0a0/merged INFO: umounting image registry.fedoraproject.org/fedora:39 (/var/lib/containers/storage/overlay/8762d4e942255ae5f22c1ca5cdcbea9118d53523b90ef15d705fc17a7574e0a0/merged) with podman image umount INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 2.3 MB/s | 23 MB 00:10 Additional repo http_kojipkgs_fedoraproject_org 13 MB/s | 68 MB 00:05 fedora 50 MB/s | 79 MB 00:01 updates 17 MB/s | 24 MB 00:01 Last metadata expiration check: 0:00:08 ago on Tue Jan 30 03:58:04 2024. Package python3-dnf-4.18.1-2.fc39.noarch is already installed. Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing: python3-dnf-plugins-core noarch 4.4.4-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 302 k Upgrading: dnf noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 496 k dnf-data noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k python3-dnf noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 549 k yum noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k Installing dependencies: dbus-libs s390x 1:1.14.10-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 159 k python3-dateutil noarch 1:2.8.2-13.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 345 k python3-dbus s390x 1.3.2-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 146 k python3-distro noarch 1.9.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 45 k python3-six noarch 1.16.0-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k python3-systemd s390x 235-9.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 100 k Transaction Summary ========================================================================================================================= Install 7 Packages Upgrade 4 Packages Total download size: 2.2 M Downloading Packages: (1/11): python3-dbus-1.3.2-6.fc40.s390x.rpm 1.1 MB/s | 146 kB 00:00 (2/11): python3-distro-1.9.0-3.fc40.noarch.rpm 10 MB/s | 45 kB 00:00 (3/11): dbus-libs-1.14.10-3.fc40.s390x.rpm 1.1 MB/s | 159 kB 00:00 (4/11): python3-dateutil-2.8.2-13.fc40.noarch.r 2.4 MB/s | 345 kB 00:00 (5/11): python3-dnf-plugins-core-4.4.4-3.fc40.n 44 MB/s | 302 kB 00:00 (6/11): python3-six-1.16.0-14.fc40.noarch.rpm 5.5 MB/s | 41 kB 00:00 (7/11): python3-systemd-235-9.fc40.s390x.rpm 17 MB/s | 100 kB 00:00 (8/11): dnf-data-4.18.2-1.fc40.noarch.rpm 9.1 MB/s | 39 kB 00:00 (9/11): yum-4.18.2-1.fc40.noarch.rpm 8.5 MB/s | 37 kB 00:00 (10/11): dnf-4.18.2-1.fc40.noarch.rpm 29 MB/s | 496 kB 00:00 (11/11): python3-dnf-4.18.2-1.fc40.noarch.rpm 21 MB/s | 549 kB 00:00 -------------------------------------------------------------------------------- Total 13 MB/s | 2.2 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Upgrading : dnf-data-4.18.2-1.fc40.noarch 1/15 Upgrading : python3-dnf-4.18.2-1.fc40.noarch 2/15 Upgrading : dnf-4.18.2-1.fc40.noarch 3/15 Running scriptlet: dnf-4.18.2-1.fc40.noarch 3/15 Installing : python3-systemd-235-9.fc40.s390x 4/15 Installing : python3-six-1.16.0-14.fc40.noarch 5/15 Installing : python3-dateutil-1:2.8.2-13.fc40.noarch 6/15 Installing : python3-distro-1.9.0-3.fc40.noarch 7/15 Installing : dbus-libs-1:1.14.10-3.fc40.s390x 8/15 Installing : python3-dbus-1.3.2-6.fc40.s390x 9/15 Installing : python3-dnf-plugins-core-4.4.4-3.fc40.noarch 10/15 Upgrading : yum-4.18.2-1.fc40.noarch 11/15 Cleanup : yum-4.18.1-2.fc39.noarch 12/15 Running scriptlet: dnf-4.18.1-2.fc39.noarch 13/15 Cleanup : dnf-4.18.1-2.fc39.noarch 13/15 Running scriptlet: dnf-4.18.1-2.fc39.noarch 13/15 Cleanup : python3-dnf-4.18.1-2.fc39.noarch 14/15 Cleanup : dnf-data-4.18.1-2.fc39.noarch 15/15 Running scriptlet: dnf-data-4.18.1-2.fc39.noarch 15/15 Verifying : dbus-libs-1:1.14.10-3.fc40.s390x 1/15 Verifying : python3-dateutil-1:2.8.2-13.fc40.noarch 2/15 Verifying : python3-dbus-1.3.2-6.fc40.s390x 3/15 Verifying : python3-distro-1.9.0-3.fc40.noarch 4/15 Verifying : python3-dnf-plugins-core-4.4.4-3.fc40.noarch 5/15 Verifying : python3-six-1.16.0-14.fc40.noarch 6/15 Verifying : python3-systemd-235-9.fc40.s390x 7/15 Verifying : dnf-4.18.2-1.fc40.noarch 8/15 Verifying : dnf-4.18.1-2.fc39.noarch 9/15 Verifying : dnf-data-4.18.2-1.fc40.noarch 10/15 Verifying : dnf-data-4.18.1-2.fc39.noarch 11/15 Verifying : python3-dnf-4.18.2-1.fc40.noarch 12/15 Verifying : python3-dnf-4.18.1-2.fc39.noarch 13/15 Verifying : yum-4.18.2-1.fc40.noarch 14/15 Verifying : yum-4.18.1-2.fc39.noarch 15/15 Upgraded: dnf-4.18.2-1.fc40.noarch dnf-data-4.18.2-1.fc40.noarch python3-dnf-4.18.2-1.fc40.noarch yum-4.18.2-1.fc40.noarch Installed: dbus-libs-1:1.14.10-3.fc40.s390x python3-dateutil-1:2.8.2-13.fc40.noarch python3-dbus-1.3.2-6.fc40.s390x python3-distro-1.9.0-3.fc40.noarch python3-dnf-plugins-core-4.4.4-3.fc40.noarch python3-six-1.16.0-14.fc40.noarch python3-systemd-235-9.fc40.s390x Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-s390x-1706587007.973351/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-1.fc39.s390x rpm-sequoia-1.5.0-1.fc39.s390x python3-dnf-4.18.2-1.fc40.noarch python3-dnf-plugins-core-4.4.4-3.fc40.noarch yum-4.18.2-1.fc40.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 17 MB/s | 23 MB 00:01 Additional repo http_kojipkgs_fedoraproject_org 260 MB/s | 68 MB 00:00 fedora 10 MB/s | 79 MB 00:07 updates 33 MB/s | 24 MB 00:00 Last metadata expiration check: 0:00:06 ago on Tue Jan 30 03:59:24 2024. Dependencies resolved. ======================================================================================================================================== Package Arch Version Repository Size ======================================================================================================================================== Installing group/module packages: bash s390x 5.2.26-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 M bzip2 s390x 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 53 k coreutils s390x 9.4-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M cpio s390x 2.15-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 291 k diffutils s390x 3.10-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 412 k fedora-release-common noarch 40-0.29 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k findutils s390x 1:4.9.0-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 493 k gawk s390x 5.3.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M glibc-minimal-langpack s390x 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 96 k grep s390x 3.11-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 297 k gzip s390x 1.12-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 167 k info s390x 7.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 195 k patch s390x 2.7.6-24.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 141 k redhat-rpm-config noarch 280-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 75 k rpm-build s390x 4.19.1-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 71 k sed s390x 4.8-15.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 302 k shadow-utils s390x 2:4.14.0-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M tar s390x 2:1.35-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 871 k unzip s390x 6.0-63.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 195 k util-linux s390x 2.39.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M which s390x 2.21-41.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 43 k xz s390x 5.4.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 533 k Installing dependencies: alternatives s390x 1.26-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k ansible-srpm-macros noarch 1-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k audit-libs s390x 4.0-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 125 k authselect s390x 1.5.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 143 k authselect-libs s390x 1.5.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 233 k basesystem noarch 11-20.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.2 k binutils s390x 2.41-31.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 5.9 M binutils-gold s390x 2.41-31.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 996 k bzip2-libs s390x 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 47 k ca-certificates noarch 2023.2.62_v7.0.401-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 862 k coreutils-common s390x 9.4-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.1 M cracklib s390x 2.9.11-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 84 k crypto-policies noarch 20231204-3.git1e3a2e4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 69 k curl s390x 8.5.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 373 k cyrus-sasl-lib s390x 2.1.28-19.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 821 k debugedit s390x 5.0-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 82 k dwz s390x 0.15-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 144 k ed s390x 1.20-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 84 k efi-srpm-macros noarch 5-11.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k elfutils s390x 0.190-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 575 k elfutils-debuginfod-client s390x 0.190-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 38 k elfutils-default-yama-scope noarch 0.190-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k elfutils-libelf s390x 0.190-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 200 k elfutils-libs s390x 0.190-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 278 k 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s390x 0.8.2-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 36 k xz-libs s390x 5.4.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 116 k zig-srpm-macros noarch 1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.0 k zip s390x 3.0-40.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 283 k zlib-ng-compat s390x 2.1.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 66 k zstd s390x 1.5.5-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 511 k Installing Groups: Buildsystem building group Transaction Summary ======================================================================================================================================== Install 152 Packages Total download size: 52 M Installed size: 179 M Downloading Packages: (1/152): ansible-srpm-macros-1-14.fc40.noarch.r 820 kB/s | 21 kB 00:00 (2/152): audit-libs-4.0-7.fc40.s390x.rpm 24 MB/s | 125 kB 00:00 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00:00 (63/152): libarchive-3.7.2-3.fc40.s390x.rpm 40 MB/s | 442 kB 00:00 (64/152): libblkid-2.39.3-4.fc40.s390x.rpm 21 MB/s | 121 kB 00:00 (65/152): libcap-2.69-3.fc40.s390x.rpm 15 MB/s | 85 kB 00:00 (66/152): libbrotli-1.1.0-3.fc40.s390x.rpm 43 MB/s | 387 kB 00:00 (67/152): libcap-ng-0.8.4-4.fc40.s390x.rpm 6.8 MB/s | 33 kB 00:00 (68/152): libcom_err-1.47.0-4.fc40.s390x.rpm 6.7 MB/s | 26 kB 00:00 (69/152): libcurl-8.5.0-2.fc40.s390x.rpm 56 MB/s | 364 kB 00:00 (70/152): libeconf-0.5.2-3.fc40.s390x.rpm 6.8 MB/s | 32 kB 00:00 (71/152): libevent-2.1.12-11.fc40.s390x.rpm 48 MB/s | 260 kB 00:00 (72/152): libfdisk-2.39.3-4.fc40.s390x.rpm 29 MB/s | 166 kB 00:00 (73/152): libffi-3.4.4-7.fc40.s390x.rpm 9.5 MB/s | 36 kB 00:00 (74/152): libgcc-14.0.1-0.4.fc40.s390x.rpm 17 MB/s | 70 kB 00:00 (75/152): libidn2-2.3.7-1.fc40.s390x.rpm 28 MB/s | 113 kB 00:00 (76/152): libgomp-14.0.1-0.4.fc40.s390x.rpm 58 MB/s | 336 kB 00:00 (77/152): libnghttp2-1.59.0-2.fc40.s390x.rpm 20 MB/s | 79 kB 00:00 (78/152): libmount-2.39.3-4.fc40.s390x.rpm 32 MB/s | 159 kB 00:00 (79/152): libnsl2-2.0.1-1.fc40.s390x.rpm 7.4 MB/s | 29 kB 00:00 (80/152): libpkgconf-1.9.5-4.fc40.s390x.rpm 9.1 MB/s | 38 kB 00:00 (81/152): libpsl-0.21.5-3.fc40.s390x.rpm 15 MB/s | 64 kB 00:00 (82/152): libpwquality-1.4.5-9.fc40.s390x.rpm 25 MB/s | 109 kB 00:00 (83/152): libselinux-3.6-4.fc40.s390x.rpm 22 MB/s | 92 kB 00:00 (84/152): libsemanage-3.6-3.fc40.s390x.rpm 30 MB/s | 120 kB 00:00 (85/152): libsmartcols-2.39.3-4.fc40.s390x.rpm 15 MB/s | 70 kB 00:00 (86/152): libsepol-3.6-3.fc40.s390x.rpm 46 MB/s | 349 kB 00:00 (87/152): libssh-config-0.10.6-4.fc40.noarch.rp 2.8 MB/s | 9.0 kB 00:00 (88/152): libssh-0.10.6-4.fc40.s390x.rpm 36 MB/s | 209 kB 00:00 (89/152): libtasn1-4.19.0-6.fc40.s390x.rpm 17 MB/s | 78 kB 00:00 (90/152): libstdc++-14.0.1-0.4.fc40.s390x.rpm 104 MB/s | 975 kB 00:00 (91/152): libtirpc-1.3.4-1.rc2.fc40.2.s390x.rpm 21 MB/s | 96 kB 00:00 (92/152): libutempter-1.2.1-13.fc40.s390x.rpm 6.9 MB/s | 26 kB 00:00 (93/152): 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gdb-minimal-14.1-8.fc40.s390x.rpm 6.4 MB/s | 4.2 MB 00:00 -------------------------------------------------------------------------------- Total 78 MB/s | 52 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-8.fc40.s390x 1/1 Preparing : 1/1 Installing : libgcc-14.0.1-0.4.fc40.s390x 1/152 Running scriptlet: libgcc-14.0.1-0.4.fc40.s390x 1/152 Installing : crypto-policies-20231204-3.git1e3a2e4.fc40.noarc 2/152 Running scriptlet: crypto-policies-20231204-3.git1e3a2e4.fc40.noarc 2/152 Installing : fedora-release-identity-basic-40-0.29.noarch 3/152 Installing : fedora-repos-rawhide-40-0.2.noarch 4/152 Installing : fedora-gpg-keys-40-0.2.noarch 5/152 Installing : fedora-repos-40-0.2.noarch 6/152 Installing : fedora-release-common-40-0.29.noarch 7/152 Installing : fedora-release-40-0.29.noarch 8/152 Installing : setup-2.14.5-2.fc40.noarch 9/152 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.5-2.fc40.noarch 9/152 Installing : filesystem-3.18-8.fc40.s390x 10/152 Installing : basesystem-11-20.fc40.noarch 11/152 Installing : rust-srpm-macros-25.2-3.fc40.noarch 12/152 Installing : qt6-srpm-macros-6.6.1-5.fc40.noarch 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Installing : patch-2.7.6-24.fc40.s390x 88/152 Installing : elfutils-default-yama-scope-0.190-6.fc40.noarch 89/152 Running scriptlet: elfutils-default-yama-scope-0.190-6.fc40.noarch 89/152 Installing : cpio-2.15-1.fc40.s390x 90/152 Installing : diffutils-3.10-5.fc40.s390x 91/152 Installing : keyutils-libs-1.6.3-3.fc40.s390x 92/152 Installing : libbrotli-1.1.0-3.fc40.s390x 93/152 Installing : libffi-3.4.4-7.fc40.s390x 94/152 Installing : p11-kit-0.25.3-1.fc40.s390x 95/152 Installing : p11-kit-trust-0.25.3-1.fc40.s390x 96/152 Running scriptlet: p11-kit-trust-0.25.3-1.fc40.s390x 96/152 Installing : libgomp-14.0.1-0.4.fc40.s390x 97/152 Installing : libnghttp2-1.59.0-2.fc40.s390x 98/152 Installing : libpkgconf-1.9.5-4.fc40.s390x 99/152 Installing : pkgconf-1.9.5-4.fc40.s390x 100/152 Installing : pkgconf-pkg-config-1.9.5-4.fc40.s390x 101/152 Installing : libverto-0.3.2-8.fc40.s390x 102/152 Installing : xxhash-libs-0.8.2-2.fc40.s390x 103/152 Installing : libssh-config-0.10.6-4.fc40.noarch 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rpm-libs-4.19.1-4.fc40.s390x 136/152 Running scriptlet: rpm-4.19.1-4.fc40.s390x 137/152 Installing : rpm-4.19.1-4.fc40.s390x 137/152 Installing : efi-srpm-macros-5-11.fc40.noarch 138/152 Installing : lua-srpm-macros-1-11.fc40.noarch 139/152 Installing : zig-srpm-macros-1-2.fc40.noarch 140/152 Installing : rpm-build-libs-4.19.1-4.fc40.s390x 141/152 Installing : ansible-srpm-macros-1-14.fc40.noarch 142/152 Installing : fonts-srpm-macros-1:2.0.5-14.fc40.noarch 143/152 Installing : forge-srpm-macros-0.2.0-3.fc40.noarch 144/152 Installing : go-srpm-macros-3.3.1-3.fc40.noarch 145/152 Installing : python-srpm-macros-3.12-7.fc40.noarch 146/152 Installing : redhat-rpm-config-280-1.fc40.noarch 147/152 Installing : rpm-build-4.19.1-4.fc40.s390x 148/152 Installing : pyproject-srpm-macros-1.12.0-1.fc40.noarch 149/152 Installing : util-linux-2.39.3-4.fc40.s390x 150/152 Installing : which-2.21-41.fc40.s390x 151/152 Installing : info-7.1-2.fc40.s390x 152/152 Running scriptlet: filesystem-3.18-8.fc40.s390x 152/152 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch 152/152 Running scriptlet: authselect-libs-1.5.0-3.fc40.s390x 152/152 Running scriptlet: rpm-4.19.1-4.fc40.s390x 152/152 Running scriptlet: info-7.1-2.fc40.s390x 152/152 Installed: alternatives-1.26-3.fc40.s390x ansible-srpm-macros-1-14.fc40.noarch audit-libs-4.0-7.fc40.s390x authselect-1.5.0-3.fc40.s390x authselect-libs-1.5.0-3.fc40.s390x basesystem-11-20.fc40.noarch bash-5.2.26-2.fc40.s390x binutils-2.41-31.fc40.s390x binutils-gold-2.41-31.fc40.s390x bzip2-1.0.8-18.fc40.s390x bzip2-libs-1.0.8-18.fc40.s390x ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch coreutils-9.4-5.fc40.s390x coreutils-common-9.4-5.fc40.s390x cpio-2.15-1.fc40.s390x cracklib-2.9.11-5.fc40.s390x crypto-policies-20231204-3.git1e3a2e4.fc40.noarch curl-8.5.0-2.fc40.s390x cyrus-sasl-lib-2.1.28-19.fc40.s390x debugedit-5.0-14.fc40.s390x diffutils-3.10-5.fc40.s390x dwz-0.15-5.fc40.s390x ed-1.20-2.fc40.s390x efi-srpm-macros-5-11.fc40.noarch elfutils-0.190-6.fc40.s390x elfutils-debuginfod-client-0.190-6.fc40.s390x elfutils-default-yama-scope-0.190-6.fc40.noarch elfutils-libelf-0.190-6.fc40.s390x elfutils-libs-0.190-6.fc40.s390x fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.29.noarch fedora-release-common-40-0.29.noarch fedora-release-identity-basic-40-0.29.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-3.fc40.s390x file-libs-5.45-3.fc40.s390x filesystem-3.18-8.fc40.s390x findutils-1:4.9.0-8.fc40.s390x fonts-srpm-macros-1:2.0.5-14.fc40.noarch forge-srpm-macros-0.2.0-3.fc40.noarch fpc-srpm-macros-1.3-12.fc40.noarch gawk-5.3.0-3.fc40.s390x gdb-minimal-14.1-8.fc40.s390x gdbm-1:1.23-6.fc40.s390x gdbm-libs-1:1.23-6.fc40.s390x ghc-srpm-macros-1.6.1-5.fc40.noarch glibc-2.38.9000-35.fc40.s390x glibc-common-2.38.9000-35.fc40.s390x glibc-gconv-extra-2.38.9000-35.fc40.s390x glibc-minimal-langpack-2.38.9000-35.fc40.s390x gmp-1:6.2.1-8.fc40.s390x gnat-srpm-macros-6-5.fc40.noarch go-srpm-macros-3.3.1-3.fc40.noarch grep-3.11-7.fc40.s390x gzip-1.12-8.fc40.s390x info-7.1-2.fc40.s390x jansson-2.13.1-9.fc40.s390x kernel-srpm-macros-1.0-22.fc40.noarch keyutils-libs-1.6.3-3.fc40.s390x krb5-libs-1.21.2-5.fc40.s390x libacl-2.3.2-1.fc40.s390x libarchive-3.7.2-3.fc40.s390x libattr-2.5.2-3.fc40.s390x libblkid-2.39.3-4.fc40.s390x libbrotli-1.1.0-3.fc40.s390x libcap-2.69-3.fc40.s390x libcap-ng-0.8.4-4.fc40.s390x libcom_err-1.47.0-4.fc40.s390x libcurl-8.5.0-2.fc40.s390x libeconf-0.5.2-3.fc40.s390x libevent-2.1.12-11.fc40.s390x libfdisk-2.39.3-4.fc40.s390x libffi-3.4.4-7.fc40.s390x libgcc-14.0.1-0.4.fc40.s390x libgomp-14.0.1-0.4.fc40.s390x libidn2-2.3.7-1.fc40.s390x libmount-2.39.3-4.fc40.s390x libnghttp2-1.59.0-2.fc40.s390x libnsl2-2.0.1-1.fc40.s390x libpkgconf-1.9.5-4.fc40.s390x libpsl-0.21.5-3.fc40.s390x libpwquality-1.4.5-9.fc40.s390x libselinux-3.6-4.fc40.s390x libsemanage-3.6-3.fc40.s390x libsepol-3.6-3.fc40.s390x libsmartcols-2.39.3-4.fc40.s390x libssh-0.10.6-4.fc40.s390x libssh-config-0.10.6-4.fc40.noarch libstdc++-14.0.1-0.4.fc40.s390x libtasn1-4.19.0-6.fc40.s390x libtirpc-1.3.4-1.rc2.fc40.2.s390x libunistring-1.1-7.fc40.s390x libutempter-1.2.1-13.fc40.s390x libuuid-2.39.3-4.fc40.s390x libverto-0.3.2-8.fc40.s390x libxcrypt-4.4.36-5.fc40.s390x libxml2-2.12.4-3.fc40.s390x libzstd-1.5.5-5.fc40.s390x lua-libs-5.4.6-5.fc40.s390x lua-srpm-macros-1-11.fc40.noarch lz4-libs-1.9.4-6.fc40.s390x mpfr-4.2.1-3.fc40.s390x ncurses-base-6.4-11.20240113.fc40.noarch ncurses-libs-6.4-11.20240113.fc40.s390x ocaml-srpm-macros-9-3.fc40.noarch openblas-srpm-macros-2-16.fc40.noarch openldap-2.6.6-1.fc39.s390x openssl-libs-1:3.1.4-4.fc40.s390x p11-kit-0.25.3-1.fc40.s390x p11-kit-trust-0.25.3-1.fc40.s390x package-notes-srpm-macros-0.5-11.fc40.noarch pam-1.6.0-1.fc40.s390x pam-libs-1.6.0-1.fc40.s390x patch-2.7.6-24.fc40.s390x pcre2-10.42-2.fc40.2.s390x pcre2-syntax-10.42-2.fc40.2.noarch perl-srpm-macros-1-53.fc40.noarch pkgconf-1.9.5-4.fc40.s390x pkgconf-m4-1.9.5-4.fc40.noarch pkgconf-pkg-config-1.9.5-4.fc40.s390x popt-1.19-6.fc40.s390x publicsuffix-list-dafsa-20240107-3.fc40.noarch pyproject-srpm-macros-1.12.0-1.fc40.noarch python-srpm-macros-3.12-7.fc40.noarch qt5-srpm-macros-5.15.12-3.fc40.noarch qt6-srpm-macros-6.6.1-5.fc40.noarch readline-8.2-8.fc40.s390x redhat-rpm-config-280-1.fc40.noarch rpm-4.19.1-4.fc40.s390x rpm-build-4.19.1-4.fc40.s390x rpm-build-libs-4.19.1-4.fc40.s390x rpm-libs-4.19.1-4.fc40.s390x rpm-sequoia-1.6.0-2.fc40.s390x rust-srpm-macros-25.2-3.fc40.noarch sed-4.8-15.fc40.s390x setup-2.14.5-2.fc40.noarch shadow-utils-2:4.14.0-4.fc40.s390x sqlite-libs-3.45.0-2.fc40.s390x systemd-libs-255.3-1.fc40.s390x tar-2:1.35-3.fc40.s390x unzip-6.0-63.fc40.s390x util-linux-2.39.3-4.fc40.s390x util-linux-core-2.39.3-4.fc40.s390x which-2.21-41.fc40.s390x xxhash-libs-0.8.2-2.fc40.s390x xz-5.4.6-1.fc40.s390x xz-libs-5.4.6-1.fc40.s390x zig-srpm-macros-1-2.fc40.noarch zip-3.0-40.fc40.s390x zlib-ng-compat-2.1.6-2.fc40.s390x zstd-1.5.5-5.fc40.s390x Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.26-3.fc40.s390x ansible-srpm-macros-1-14.fc40.noarch audit-libs-4.0-7.fc40.s390x authselect-1.5.0-3.fc40.s390x authselect-libs-1.5.0-3.fc40.s390x basesystem-11-20.fc40.noarch bash-5.2.26-2.fc40.s390x binutils-2.41-31.fc40.s390x binutils-gold-2.41-31.fc40.s390x bzip2-1.0.8-18.fc40.s390x bzip2-libs-1.0.8-18.fc40.s390x ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch coreutils-9.4-5.fc40.s390x coreutils-common-9.4-5.fc40.s390x cpio-2.15-1.fc40.s390x cracklib-2.9.11-5.fc40.s390x crypto-policies-20231204-3.git1e3a2e4.fc40.noarch curl-8.5.0-2.fc40.s390x cyrus-sasl-lib-2.1.28-19.fc40.s390x debugedit-5.0-14.fc40.s390x diffutils-3.10-5.fc40.s390x dwz-0.15-5.fc40.s390x ed-1.20-2.fc40.s390x efi-srpm-macros-5-11.fc40.noarch elfutils-0.190-6.fc40.s390x elfutils-debuginfod-client-0.190-6.fc40.s390x elfutils-default-yama-scope-0.190-6.fc40.noarch elfutils-libelf-0.190-6.fc40.s390x elfutils-libs-0.190-6.fc40.s390x fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.29.noarch fedora-release-common-40-0.29.noarch fedora-release-identity-basic-40-0.29.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-3.fc40.s390x file-libs-5.45-3.fc40.s390x filesystem-3.18-8.fc40.s390x findutils-4.9.0-8.fc40.s390x fonts-srpm-macros-2.0.5-14.fc40.noarch forge-srpm-macros-0.2.0-3.fc40.noarch fpc-srpm-macros-1.3-12.fc40.noarch gawk-5.3.0-3.fc40.s390x gdb-minimal-14.1-8.fc40.s390x gdbm-1.23-6.fc40.s390x gdbm-libs-1.23-6.fc40.s390x ghc-srpm-macros-1.6.1-5.fc40.noarch glibc-2.38.9000-35.fc40.s390x glibc-common-2.38.9000-35.fc40.s390x glibc-gconv-extra-2.38.9000-35.fc40.s390x glibc-minimal-langpack-2.38.9000-35.fc40.s390x gmp-6.2.1-8.fc40.s390x gnat-srpm-macros-6-5.fc40.noarch go-srpm-macros-3.3.1-3.fc40.noarch grep-3.11-7.fc40.s390x gzip-1.12-8.fc40.s390x info-7.1-2.fc40.s390x jansson-2.13.1-9.fc40.s390x kernel-srpm-macros-1.0-22.fc40.noarch keyutils-libs-1.6.3-3.fc40.s390x krb5-libs-1.21.2-5.fc40.s390x libacl-2.3.2-1.fc40.s390x libarchive-3.7.2-3.fc40.s390x libattr-2.5.2-3.fc40.s390x libblkid-2.39.3-4.fc40.s390x libbrotli-1.1.0-3.fc40.s390x libcap-2.69-3.fc40.s390x libcap-ng-0.8.4-4.fc40.s390x libcom_err-1.47.0-4.fc40.s390x libcurl-8.5.0-2.fc40.s390x libeconf-0.5.2-3.fc40.s390x libevent-2.1.12-11.fc40.s390x libfdisk-2.39.3-4.fc40.s390x libffi-3.4.4-7.fc40.s390x libgcc-14.0.1-0.4.fc40.s390x libgomp-14.0.1-0.4.fc40.s390x libidn2-2.3.7-1.fc40.s390x libmount-2.39.3-4.fc40.s390x libnghttp2-1.59.0-2.fc40.s390x libnsl2-2.0.1-1.fc40.s390x libpkgconf-1.9.5-4.fc40.s390x libpsl-0.21.5-3.fc40.s390x libpwquality-1.4.5-9.fc40.s390x libselinux-3.6-4.fc40.s390x libsemanage-3.6-3.fc40.s390x libsepol-3.6-3.fc40.s390x libsmartcols-2.39.3-4.fc40.s390x libssh-0.10.6-4.fc40.s390x libssh-config-0.10.6-4.fc40.noarch libstdc++-14.0.1-0.4.fc40.s390x libtasn1-4.19.0-6.fc40.s390x libtirpc-1.3.4-1.rc2.fc40.2.s390x libunistring-1.1-7.fc40.s390x libutempter-1.2.1-13.fc40.s390x libuuid-2.39.3-4.fc40.s390x libverto-0.3.2-8.fc40.s390x libxcrypt-4.4.36-5.fc40.s390x libxml2-2.12.4-3.fc40.s390x libzstd-1.5.5-5.fc40.s390x lua-libs-5.4.6-5.fc40.s390x lua-srpm-macros-1-11.fc40.noarch lz4-libs-1.9.4-6.fc40.s390x mpfr-4.2.1-3.fc40.s390x ncurses-base-6.4-11.20240113.fc40.noarch ncurses-libs-6.4-11.20240113.fc40.s390x ocaml-srpm-macros-9-3.fc40.noarch openblas-srpm-macros-2-16.fc40.noarch openldap-2.6.6-1.fc39.s390x openssl-libs-3.1.4-4.fc40.s390x p11-kit-0.25.3-1.fc40.s390x p11-kit-trust-0.25.3-1.fc40.s390x package-notes-srpm-macros-0.5-11.fc40.noarch pam-1.6.0-1.fc40.s390x pam-libs-1.6.0-1.fc40.s390x patch-2.7.6-24.fc40.s390x pcre2-10.42-2.fc40.2.s390x pcre2-syntax-10.42-2.fc40.2.noarch perl-srpm-macros-1-53.fc40.noarch pkgconf-1.9.5-4.fc40.s390x pkgconf-m4-1.9.5-4.fc40.noarch pkgconf-pkg-config-1.9.5-4.fc40.s390x popt-1.19-6.fc40.s390x publicsuffix-list-dafsa-20240107-3.fc40.noarch pyproject-srpm-macros-1.12.0-1.fc40.noarch python-srpm-macros-3.12-7.fc40.noarch qt5-srpm-macros-5.15.12-3.fc40.noarch qt6-srpm-macros-6.6.1-5.fc40.noarch readline-8.2-8.fc40.s390x redhat-rpm-config-280-1.fc40.noarch rpm-4.19.1-4.fc40.s390x rpm-build-4.19.1-4.fc40.s390x rpm-build-libs-4.19.1-4.fc40.s390x rpm-libs-4.19.1-4.fc40.s390x rpm-sequoia-1.6.0-2.fc40.s390x rust-srpm-macros-25.2-3.fc40.noarch sed-4.8-15.fc40.s390x setup-2.14.5-2.fc40.noarch shadow-utils-4.14.0-4.fc40.s390x sqlite-libs-3.45.0-2.fc40.s390x systemd-libs-255.3-1.fc40.s390x tar-1.35-3.fc40.s390x unzip-6.0-63.fc40.s390x util-linux-2.39.3-4.fc40.s390x util-linux-core-2.39.3-4.fc40.s390x which-2.21-41.fc40.s390x xxhash-libs-0.8.2-2.fc40.s390x xz-5.4.6-1.fc40.s390x xz-libs-5.4.6-1.fc40.s390x zig-srpm-macros-1-2.fc40.noarch zip-3.0-40.fc40.s390x zlib-ng-compat-2.1.6-2.fc40.s390x zstd-1.5.5-5.fc40.s390x Start: buildsrpm Start: rpmbuild -bs Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1706486400 Wrote: /builddir/build/SRPMS/seqan2-2.4.0-22.fc40.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-s390x-1706587007.973351/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-s390x-1706587007.973351/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-s390x-1706587007.973351/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-40ad8ut2/seqan2/seqan2.spec) Config(child) 3 minutes 6 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/seqan2-2.4.0-22.fc40.src.rpm) Config(fedora-39-s390x) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-s390x-bootstrap-1706587007.973351/root. INFO: reusing tmpfs at /var/lib/mock/fedora-39-s390x-bootstrap-1706587007.973351/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-s390x-1706587007.973351/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-1.fc39.s390x rpm-sequoia-1.5.0-1.fc39.s390x python3-dnf-4.18.2-1.fc40.noarch python3-dnf-plugins-core-4.4.4-3.fc40.noarch yum-4.18.2-1.fc40.noarch Finish: chroot init Start: build phase for seqan2-2.4.0-22.fc40.src.rpm Start: build setup for seqan2-2.4.0-22.fc40.src.rpm Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1706486400 Wrote: /builddir/build/SRPMS/seqan2-2.4.0-22.fc40.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 3.5 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 121 kB/s | 3.8 kB 00:00 fedora 23 kB/s | 3.8 kB 00:00 updates 38 kB/s | 4.3 kB 00:00 Dependencies resolved. ================================================================================================================================== Package Arch Version Repository Size ================================================================================================================================== Installing: boost-devel s390x 1.83.0-2.fc40 copr_base 12 M bzip2-devel s390x 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 213 k cmake s390x 3.27.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.8 M gcc-c++ s390x 14.0.1-0.4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 12 M libstdc++-static s390x 14.0.1-0.4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 M llvm-devel s390x 17.0.6-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.6 M make s390x 1:4.4.1-6.fc40 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================================================================================================================================== Install 200 Packages Total download size: 296 M Installed size: 1.4 G Downloading Packages: (1/200): boost-1.83.0-2.fc40.s390x.rpm 83 kB/s | 14 kB 00:00 (2/200): boost-atomic-1.83.0-2.fc40.s390x.rpm 101 kB/s | 20 kB 00:00 (3/200): boost-chrono-1.83.0-2.fc40.s390x.rpm 132 kB/s | 26 kB 00:00 (4/200): boost-container-1.83.0-2.fc40.s390x.rp 535 kB/s | 42 kB 00:00 (5/200): boost-context-1.83.0-2.fc40.s390x.rpm 182 kB/s | 17 kB 00:00 (6/200): boost-contract-1.83.0-2.fc40.s390x.rpm 397 kB/s | 46 kB 00:00 (7/200): boost-coroutine-1.83.0-2.fc40.s390x.rp 289 kB/s | 21 kB 00:00 (8/200): boost-date-time-1.83.0-2.fc40.s390x.rp 268 kB/s | 16 kB 00:00 (9/200): boost-fiber-1.83.0-2.fc40.s390x.rpm 192 kB/s | 43 kB 00:00 (10/200): boost-filesystem-1.83.0-2.fc40.s390x. 337 kB/s | 69 kB 00:00 (11/200): boost-graph-1.83.0-2.fc40.s390x.rpm 1.2 MB/s | 160 kB 00:00 (12/200): boost-iostreams-1.83.0-2.fc40.s390x.r 316 kB/s | 41 kB 00:00 (13/200): boost-devel-1.83.0-2.fc40.s390x.rpm 25 MB/s | 12 MB 00:00 (14/200): boost-json-1.83.0-2.fc40.s390x.rpm 1.4 MB/s | 156 kB 00:00 (15/200): boost-locale-1.83.0-2.fc40.s390x.rpm 2.0 MB/s | 219 kB 00:00 (16/200): boost-log-1.83.0-2.fc40.s390x.rpm 8.3 MB/s | 502 kB 00:00 (17/200): boost-math-1.83.0-2.fc40.s390x.rpm 4.0 MB/s | 242 kB 00:00 (18/200): boost-nowide-1.83.0-2.fc40.s390x.rpm 354 kB/s | 21 kB 00:00 (19/200): boost-numpy3-1.83.0-2.fc40.s390x.rpm 530 kB/s | 30 kB 00:00 (20/200): boost-python3-1.83.0-2.fc40.s390x.rpm 1.6 MB/s | 95 kB 00:00 (21/200): boost-program-options-1.83.0-2.fc40.s 1.9 MB/s | 112 kB 00:00 (22/200): boost-random-1.83.0-2.fc40.s390x.rpm 434 kB/s | 25 kB 00:00 (23/200): boost-regex-1.83.0-2.fc40.s390x.rpm 2.1 MB/s | 125 kB 00:00 (24/200): boost-serialization-1.83.0-2.fc40.s39 1.2 MB/s | 138 kB 00:00 (25/200): boost-stacktrace-1.83.0-2.fc40.s390x. 544 kB/s | 31 kB 00:00 (26/200): boost-system-1.83.0-2.fc40.s390x.rpm 290 kB/s | 16 kB 00:00 (27/200): boost-thread-1.83.0-2.fc40.s390x.rpm 1.1 MB/s | 63 kB 00:00 (28/200): boost-timer-1.83.0-2.fc40.s390x.rpm 389 kB/s | 22 kB 00:00 (29/200): boost-test-1.83.0-2.fc40.s390x.rpm 4.1 MB/s | 251 kB 00:00 (30/200): boost-type_erasure-1.83.0-2.fc40.s390 606 kB/s | 34 kB 00:00 (31/200): flexiblas-3.4.1-3.fc40.s390x.rpm 459 kB/s | 25 kB 00:00 (32/200): boost-wave-1.83.0-2.fc40.s390x.rpm 3.9 MB/s | 227 kB 00:00 (33/200): flexiblas-openblas-openmp-3.4.1-3.fc4 318 kB/s | 18 kB 00:00 (34/200): graphite2-1.3.14-15.fc40.s390x.rpm 1.5 MB/s | 101 kB 00:00 (35/200): flexiblas-netlib-3.4.1-3.fc40.s390x.r 31 MB/s | 3.7 MB 00:00 (36/200): abattis-cantarell-vf-fonts-0.301-12.f 5.6 MB/s | 120 kB 00:00 (37/200): alsa-lib-1.2.11-2.fc40.s390x.rpm 46 MB/s | 525 kB 00:00 (38/200): annobin-docs-12.38-1.fc40.noarch.rpm 19 MB/s | 90 kB 00:00 (39/200): annobin-plugin-gcc-12.38-1.fc40.s390x 73 MB/s | 956 kB 00:00 (40/200): brotli-1.1.0-3.fc40.s390x.rpm 5.4 MB/s | 20 kB 00:00 (41/200): brotli-devel-1.1.0-3.fc40.s390x.rpm 9.7 MB/s | 34 kB 00:00 (42/200): bzip2-devel-1.0.8-18.fc40.s390x.rpm 45 MB/s | 213 kB 00:00 (43/200): cairo-1.18.0-3.fc40.s390x.rpm 94 MB/s | 729 kB 00:00 (44/200): cmake-3.27.7-1.fc40.s390x.rpm 242 MB/s | 7.8 MB 00:00 (45/200): cmake-data-3.27.7-1.fc40.noarch.rpm 129 MB/s | 1.7 MB 00:00 (46/200): cmake-filesystem-3.27.7-1.fc40.s390x. 4.9 MB/s | 19 kB 00:00 (47/200): cmake-rpm-macros-3.27.7-1.fc40.noarch 4.9 MB/s | 19 kB 00:00 (48/200): python3-numpy-1.26.2-4.fc40.s390x.rpm 37 MB/s | 6.9 MB 00:00 (49/200): graphite2-devel-1.3.14-15.fc40.s390x. 105 kB/s | 21 kB 00:00 (50/200): cpp-14.0.1-0.4.fc40.s390x.rpm 246 MB/s | 9.6 MB 00:00 (51/200): default-fonts-core-sans-4.0-11.fc40.n 1.0 MB/s | 25 kB 00:00 (52/200): dbus-libs-1.14.10-3.fc40.s390x.rpm 6.0 MB/s | 159 kB 00:00 (53/200): emacs-filesystem-29.2-3.fc40.noarch.r 2.1 MB/s | 7.8 kB 00:00 (54/200): expat-2.5.0-5.fc40.s390x.rpm 23 MB/s | 114 kB 00:00 (55/200): fontconfig-2.15.0-3.fc40.s390x.rpm 38 MB/s | 265 kB 00:00 (56/200): fontconfig-devel-2.15.0-3.fc40.s390x. 25 MB/s | 129 kB 00:00 (57/200): fonts-filesystem-2.0.5-14.fc40.noarch 2.0 MB/s | 8.2 kB 00:00 (58/200): freetype-2.13.2-1.fc40.s390x.rpm 83 MB/s | 441 kB 00:00 (59/200): gc-8.2.2-6.fc40.s390x.rpm 24 MB/s | 114 kB 00:00 (60/200): freetype-devel-2.13.2-1.fc40.s390x.rp 53 MB/s | 913 kB 00:00 (61/200): gcc-plugin-annobin-14.0.1-0.4.fc40.s3 3.9 MB/s | 34 kB 00:00 (62/200): gettext-0.22-4.fc40.s390x.rpm 48 MB/s | 1.1 MB 00:00 (63/200): gcc-c++-14.0.1-0.4.fc40.s390x.rpm 194 MB/s | 12 MB 00:00 (64/200): gettext-envsubst-0.22-4.fc40.s390x.rp 2.5 MB/s | 37 kB 00:00 (65/200): gettext-runtime-0.22-4.fc40.s390x.rpm 16 MB/s | 111 kB 00:00 (66/200): gettext-libs-0.22-4.fc40.s390x.rpm 35 MB/s | 352 kB 00:00 (67/200): gl-manpages-1.1-31.20190306.fc40.noar 59 MB/s | 1.0 MB 00:00 (68/200): glib2-2.79.1-1.fc40.s390x.rpm 138 MB/s | 3.0 MB 00:00 (69/200): 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gcc-plugin-annobin-14.0.1-0.4.fc40.s390x 197/200 Installing : llvm-devel-17.0.6-5.fc40.s390x 198/200 Running scriptlet: llvm-devel-17.0.6-5.fc40.s390x 198/200 Installing : python3-devel-3.12.1-4.fc40.s390x 199/200 Installing : libstdc++-static-14.0.1-0.4.fc40.s390x 200/200 Running scriptlet: fontconfig-2.15.0-3.fc40.s390x 200/200 Running scriptlet: libstdc++-static-14.0.1-0.4.fc40.s390x 200/200 Installed: abattis-cantarell-vf-fonts-0.301-12.fc40.noarch alsa-lib-1.2.11-2.fc40.s390x annobin-docs-12.38-1.fc40.noarch annobin-plugin-gcc-12.38-1.fc40.s390x boost-1.83.0-2.fc40.s390x boost-atomic-1.83.0-2.fc40.s390x boost-chrono-1.83.0-2.fc40.s390x boost-container-1.83.0-2.fc40.s390x boost-context-1.83.0-2.fc40.s390x boost-contract-1.83.0-2.fc40.s390x boost-coroutine-1.83.0-2.fc40.s390x boost-date-time-1.83.0-2.fc40.s390x boost-devel-1.83.0-2.fc40.s390x boost-fiber-1.83.0-2.fc40.s390x boost-filesystem-1.83.0-2.fc40.s390x boost-graph-1.83.0-2.fc40.s390x boost-iostreams-1.83.0-2.fc40.s390x boost-json-1.83.0-2.fc40.s390x boost-locale-1.83.0-2.fc40.s390x boost-log-1.83.0-2.fc40.s390x boost-math-1.83.0-2.fc40.s390x boost-nowide-1.83.0-2.fc40.s390x boost-numpy3-1.83.0-2.fc40.s390x boost-program-options-1.83.0-2.fc40.s390x boost-python3-1.83.0-2.fc40.s390x boost-random-1.83.0-2.fc40.s390x boost-regex-1.83.0-2.fc40.s390x boost-serialization-1.83.0-2.fc40.s390x boost-stacktrace-1.83.0-2.fc40.s390x boost-system-1.83.0-2.fc40.s390x boost-test-1.83.0-2.fc40.s390x boost-thread-1.83.0-2.fc40.s390x boost-timer-1.83.0-2.fc40.s390x boost-type_erasure-1.83.0-2.fc40.s390x boost-wave-1.83.0-2.fc40.s390x brotli-1.1.0-3.fc40.s390x brotli-devel-1.1.0-3.fc40.s390x bzip2-devel-1.0.8-18.fc40.s390x cairo-1.18.0-3.fc40.s390x cmake-3.27.7-1.fc40.s390x cmake-data-3.27.7-1.fc40.noarch cmake-filesystem-3.27.7-1.fc40.s390x cmake-rpm-macros-3.27.7-1.fc40.noarch cpp-14.0.1-0.4.fc40.s390x dbus-libs-1:1.14.10-3.fc40.s390x default-fonts-core-sans-4.0-11.fc40.noarch emacs-filesystem-1:29.2-3.fc40.noarch expat-2.5.0-5.fc40.s390x flexiblas-3.4.1-3.fc40.s390x flexiblas-netlib-3.4.1-3.fc40.s390x flexiblas-openblas-openmp-3.4.1-3.fc40.s390x fontconfig-2.15.0-3.fc40.s390x fontconfig-devel-2.15.0-3.fc40.s390x fonts-filesystem-1:2.0.5-14.fc40.noarch freetype-2.13.2-1.fc40.s390x freetype-devel-2.13.2-1.fc40.s390x gc-8.2.2-6.fc40.s390x gcc-14.0.1-0.4.fc40.s390x gcc-c++-14.0.1-0.4.fc40.s390x gcc-plugin-annobin-14.0.1-0.4.fc40.s390x gettext-0.22-4.fc40.s390x gettext-envsubst-0.22-4.fc40.s390x gettext-libs-0.22-4.fc40.s390x gettext-runtime-0.22-4.fc40.s390x gl-manpages-1.1-31.20190306.fc40.noarch glib2-2.79.1-1.fc40.s390x glib2-devel-2.79.1-1.fc40.s390x glibc-devel-2.38.9000-35.fc40.s390x glibc-headers-s390-2.38.9000-35.fc40.noarch gnutls-3.8.3-2.fc40.s390x google-noto-fonts-common-20230801-6.fc40.noarch google-noto-sans-vf-fonts-20230801-6.fc40.noarch graphite2-1.3.14-15.fc40.s390x graphite2-devel-1.3.14-15.fc40.s390x guile30-3.0.7-12.fc40.s390x harfbuzz-8.3.0-4.fc40.s390x harfbuzz-devel-8.3.0-4.fc40.s390x harfbuzz-icu-8.3.0-4.fc40.s390x jbigkit-libs-2.1-29.fc40.s390x jsoncpp-1.9.5-7.fc40.s390x kernel-headers-6.8.0-0.rc1.12.fc40.1.s390x lcms2-2.16-3.fc40.s390x libICE-1.1.1-3.fc40.s390x libICE-devel-1.1.1-3.fc40.s390x libSM-1.2.4-3.fc40.s390x libSM-devel-1.2.4-3.fc40.s390x libX11-1.8.7-3.fc40.s390x libX11-common-1.8.7-3.fc40.noarch libX11-devel-1.8.7-3.fc40.s390x libX11-xcb-1.8.7-3.fc40.s390x libXau-1.0.11-6.fc40.s390x libXau-devel-1.0.11-6.fc40.s390x libXcursor-1.2.1-7.fc40.s390x libXcursor-devel-1.2.1-7.fc40.s390x libXext-1.3.5-6.fc40.s390x libXext-devel-1.3.5-6.fc40.s390x libXfixes-6.0.1-3.fc40.s390x libXfixes-devel-6.0.1-3.fc40.s390x libXft-2.3.8-6.fc40.s390x libXft-devel-2.3.8-6.fc40.s390x libXi-1.8.1-5.fc40.s390x libXi-devel-1.8.1-5.fc40.s390x libXinerama-1.1.5-6.fc40.s390x libXinerama-devel-1.1.5-6.fc40.s390x libXrandr-1.5.4-3.fc40.s390x libXrandr-devel-1.5.4-3.fc40.s390x libXrender-0.9.11-6.fc40.s390x libXrender-devel-0.9.11-6.fc40.s390x libXt-1.3.0-3.fc40.s390x libXt-devel-1.3.0-3.fc40.s390x libXv-1.0.12-3.fc40.s390x libXv-devel-1.0.12-3.fc40.s390x libXxf86vm-1.1.5-6.fc40.s390x libasan-14.0.1-0.4.fc40.s390x libatomic-14.0.1-0.4.fc40.s390x libb2-0.98.1-11.fc40.s390x libblkid-devel-2.39.3-4.fc40.s390x libdrm-2.4.120-3.fc40.s390x libedit-3.1-50.20230828cvs.fc40.s390x libedit-devel-3.1-50.20230828cvs.fc40.s390x libffi-devel-3.4.4-7.fc40.s390x libgfortran-14.0.1-0.4.fc40.s390x libglvnd-1:1.7.0-4.fc40.s390x libglvnd-core-devel-1:1.7.0-4.fc40.s390x libglvnd-devel-1:1.7.0-4.fc40.s390x libglvnd-egl-1:1.7.0-4.fc40.s390x libglvnd-gles-1:1.7.0-4.fc40.s390x libglvnd-glx-1:1.7.0-4.fc40.s390x libglvnd-opengl-1:1.7.0-4.fc40.s390x libicu-73.2-5.fc40.s390x libicu-devel-73.2-5.fc40.s390x libjpeg-turbo-2.1.4-6.fc40.s390x liblerc-4.0.0-6.fc40.s390x libmng-2.0.3-21.fc40.s390x libmount-devel-2.39.3-4.fc40.s390x libmpc-1.3.1-5.fc40.s390x libpng-2:1.6.40-3.fc40.s390x libpng-devel-2:1.6.40-3.fc40.s390x libselinux-devel-3.6-4.fc40.s390x libsepol-devel-3.6-3.fc40.s390x libstdc++-devel-14.0.1-0.4.fc40.s390x libstdc++-static-14.0.1-0.4.fc40.s390x libtiff-4.6.0-2.fc40.s390x libubsan-14.0.1-0.4.fc40.s390x libuuid-devel-2.39.3-4.fc40.s390x libuv-1:1.47.0-6.fc40.s390x libwayland-client-1.22.0-3.fc40.s390x libwayland-server-1.22.0-3.fc40.s390x libwebp-1.3.2-4.fc40.s390x libxcb-1.16-4.fc40.s390x libxcb-devel-1.16-4.fc40.s390x libxcrypt-devel-4.4.36-5.fc40.s390x libxml2-devel-2.12.4-3.fc40.s390x libxshmfence-1.3.2-3.fc40.s390x llvm-17.0.6-5.fc40.s390x llvm-devel-17.0.6-5.fc40.s390x llvm-googletest-17.0.6-5.fc40.s390x llvm-libs-17.0.6-5.fc40.s390x llvm-static-17.0.6-5.fc40.s390x llvm-test-17.0.6-5.fc40.s390x make-1:4.4.1-6.fc40.s390x mesa-libEGL-24.0.0~rc2-5.fc40.s390x mesa-libGL-24.0.0~rc2-5.fc40.s390x mesa-libGLU-9.0.3-4.fc40.s390x mesa-libGLU-devel-9.0.3-4.fc40.s390x mesa-libgbm-24.0.0~rc2-5.fc40.s390x mesa-libglapi-24.0.0~rc2-5.fc40.s390x mpdecimal-2.5.1-9.fc40.s390x ncurses-c++-libs-6.4-11.20240113.fc40.s390x ncurses-devel-6.4-11.20240113.fc40.s390x nettle-3.9.1-6.fc40.s390x openblas-0.3.26-1.fc40.s390x openblas-openmp-0.3.26-1.fc40.s390x pcre2-devel-10.42-2.fc40.2.s390x pcre2-utf16-10.42-2.fc40.2.s390x pcre2-utf32-10.42-2.fc40.2.s390x pixman-0.43.0-3.fc40.s390x pyproject-rpm-macros-1.12.0-1.fc40.noarch python-pip-wheel-23.3.2-1.fc40.noarch python-rpm-macros-3.12-7.fc40.noarch python3-3.12.1-4.fc40.s390x python3-devel-3.12.1-4.fc40.s390x python3-libs-3.12.1-4.fc40.s390x python3-numpy-1:1.26.2-4.fc40.s390x python3-packaging-23.2-4.fc40.noarch python3-rpm-generators-14-10.fc40.noarch python3-rpm-macros-3.12-7.fc40.noarch qt-1:4.8.7-76.fc40.s390x qt-common-1:4.8.7-76.fc40.noarch qt-devel-1:4.8.7-76.fc40.s390x qt-settings-39.1-5.fc40.noarch qt-x11-1:4.8.7-76.fc40.s390x rhash-1.4.3-4.fc40.s390x sysprof-capture-devel-45.1-2.fc40.s390x tzdata-2023d-3.fc40.noarch vim-filesystem-2:9.1.031-2.fc40.noarch xml-common-0.6.3-63.fc40.noarch xorg-x11-proto-devel-2023.2-4.fc40.noarch xz-devel-5.4.6-1.fc40.s390x zlib-ng-compat-devel-2.1.6-2.fc40.s390x Complete! Finish: build setup for seqan2-2.4.0-22.fc40.src.rpm Start: rpmbuild seqan2-2.4.0-22.fc40.src.rpm Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1706486400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.7SQZa0 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf seqan-seqan-v2.4.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/seqan-seqan-v2.4.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd seqan-seqan-v2.4.0 + rm -rf /builddir/build/BUILD/seqan-seqan-v2.4.0-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/seqan-seqan-v2.4.0-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/seqan-disable_stripping.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/seqan2-set_config_filepath.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/seqan2-set_awk_installation.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f + find . -perm /755 -type f '(' -name '*.cpp' -o -name '*.h' ')' -exec chmod -x '{}' ';' ++ ls apps/ ++ grep -v CMakeLists + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/alf/LICENSE apps/alf/alf-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/bs_tools/LICENSE apps/bs_tools/bs_tools-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/dfi/LICENSE apps/dfi/dfi-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/fiona/LICENSE apps/fiona/fiona-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/fx_tools/LICENSE apps/fx_tools/fx_tools-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/gustaf/LICENSE apps/gustaf/gustaf-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/insegt/LICENSE apps/insegt/insegt-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/mason2/LICENSE apps/mason2/mason2-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/micro_razers/LICENSE apps/micro_razers/micro_razers-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/ngs_roi/LICENSE apps/ngs_roi/ngs_roi-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/pair_align/LICENSE apps/pair_align/pair_align-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/param_chooser/LICENSE apps/param_chooser/param_chooser-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/rabema/LICENSE apps/rabema/rabema-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/razers/LICENSE apps/razers/razers-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/razers3/LICENSE apps/razers3/razers3-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/rep_sep/LICENSE apps/rep_sep/rep_sep-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/sak/LICENSE apps/sak/sak-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/sam2matrix/LICENSE apps/sam2matrix/sam2matrix-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/samcat/LICENSE apps/samcat/samcat-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/searchjoin/LICENSE apps/searchjoin/searchjoin-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/seqan_tcoffee/LICENSE apps/seqan_tcoffee/seqan_tcoffee-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/seqcons2/LICENSE apps/seqcons2/seqcons2-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/sgip/LICENSE apps/sgip/sgip-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/snp_store/LICENSE apps/snp_store/snp_store-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/splazers/LICENSE apps/splazers/splazers-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/stellar/LICENSE apps/stellar/stellar-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/tree_recon/LICENSE apps/tree_recon/tree_recon-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/yara/LICENSE apps/yara/yara-LICENSE + cp -p apps/rabema/COPYING apps/rabema/rabema-COPYING + rm -rf util/py_lib/seqan/dox/tpl/lib/font-awesome/css util/py_lib/seqan/dox/tpl/lib/font-awesome/fonts util/py_lib/seqan/dox/tpl/lib/font-awesome/less util/py_lib/seqan/dox/tpl/lib/font-awesome/scss + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.Cgy2Vb + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd seqan-seqan-v2.4.0 + mkdir -p build/library + pushd build/library ~/build/BUILD/seqan-seqan-v2.4.0/build/library ~/build/BUILD/seqan-seqan-v2.4.0 + SEQAN_OPT_FLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG' -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/seqan2 -DCMAKE_INSTALL_INCLUDEDIR:PATH=include/seqan2 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -DSEQAN_BUILD_SYSTEM:STRING=SEQAN_RELEASE_LIBRARY -DSEQAN_DISABLE_VERSION_CHECK:BOOL=ON -DZLIB_INCLUDE_DIR:PATH=/usr/include -DZLIB_LIBRARY:FILEPATH=/usr/lib64/libz.so -DBZIP2_INCLUDE_DIR:PATH=/usr/include -DBZIP2_LIBRARY:FILEPATH=/usr/lib64/libbz2.so -DBoost_INCLUDE_DIR:PATH=/usr/include -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3 -DSPHINX_EXECUTABLE:FILEPATH=/usr/bin/sphinx-build -DSPHINX_MAN_OUTPUT:BOOL=ON -DSPHINX_TEXT_OUTPUT:BOOL=ON -DYARA_LARGE_CONTIGS:BOOL=OFF ../.. CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The CXX compiler identification is GNU 14.0.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:16 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Initializing SeqAn Build System... -- Selected repository dir: /builddir/build/BUILD/seqan-seqan-v2.4.0 -- No revision system found. -- Repository date not determined. -- Repository revision not determined. -- Configuring dox CMake Deprecation Warning at dox/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Warning (dev) at dox/CMakeLists.txt:18 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.12.1", minimum required is "2.7") -- You need Python 2.x for building dox. (skip the tests) -- Configuring done (0.3s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: BUILD_SHARED_LIBS BZIP2_INCLUDE_DIR BZIP2_LIBRARY Boost_INCLUDE_DIR CMAKE_CXX_FLAGS_RELEASE CMAKE_C_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH CMAKE_SKIP_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SPHINX_EXECUTABLE SPHINX_MAN_OUTPUT SPHINX_TEXT_OUTPUT YARA_LARGE_CONTIGS ZLIB_INCLUDE_DIR ZLIB_LIBRARY -- Build files have been written to: /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library + /usr/bin/make -O -j2 V=1 VERBOSE=1 /usr/bin/cmake -S/builddir/build/BUILD/seqan-seqan-v2.4.0 -B/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library/CMakeFiles /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Nothing to be done for 'all'. /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library/CMakeFiles 0 + popd ~/build/BUILD/seqan-seqan-v2.4.0 + mkdir -p build/Release + pushd build/Release ~/build/BUILD/seqan-seqan-v2.4.0/build/Release ~/build/BUILD/seqan-seqan-v2.4.0 + SEQAN_OPT_FLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG' -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/seqan2 -DCMAKE_INSTALL_INCLUDEDIR:PATH=include/seqan2 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -DSEQAN_BUILD_SYSTEM:STRING=SEQAN_RELEASE_APPS -DSEQAN_DISABLE_VERSION_CHECK:BOOL=ON -DZLIB_INCLUDE_DIR:PATH=/usr/include -DZLIB_LIBRARY:FILEPATH=/usr/lib64/libz.so -DBZIP2_INCLUDE_DIR:PATH=/usr/include -DBZIP2_LIBRARY:FILEPATH=/usr/lib64/libbz2.so -DBoost_INCLUDE_DIR:PATH=/usr/include -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3 -DYARA_LARGE_CONTIGS:BOOL=OFF -DSPHINX_EXECUTABLE:FILEPATH=/usr/bin/sphinx-build -DSPHINX_MAN_OUTPUT:BOOL=ON -DSPHINX_TEXT_OUTPUT:BOOL=ON ../.. CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The CXX compiler identification is GNU 14.0.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:16 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Initializing SeqAn Build System... -- Selected repository dir: /builddir/build/BUILD/seqan-seqan-v2.4.0 -- No revision system found. -- Repository date not determined. -- Repository revision not determined. -- Configuring apps CMake Deprecation Warning at apps/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Deprecation Warning at apps/alf/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/alf -- Performing Test CXX14_BUILTIN -- Performing Test CXX14_BUILTIN - Success -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - found -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Deprecation Warning at apps/bs_tools/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/bs_tools -- Found ZLIB: /usr/lib64/libz.so (found version "1.3.0") -- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/bs_tools/CMakeLists.txt:123 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.12.1", minimum required is "2.7") CMake Deprecation Warning at apps/dfi/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/dfi -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/dfi/CMakeLists.txt:74 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/fiona/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/fiona -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/fiona/CMakeLists.txt:100 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/fx_tools/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/fx_tools -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Deprecation Warning at apps/gustaf/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/gustaf -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/gustaf/CMakeLists.txt:97 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/insegt/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/insegt -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/insegt/CMakeLists.txt:88 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/mason2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/mason2 -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/mason2/CMakeLists.txt:167 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/micro_razers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/micro_razers -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/micro_razers/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/ngs_roi/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/ngs_roi -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/ngs_roi/CMakeLists.txt:118 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/pair_align/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/pair_align -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/pair_align/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/param_chooser/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/param_chooser -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Deprecation Warning at apps/rabema/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/rabema -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/rabema/CMakeLists.txt:110 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/razers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/razers -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers/CMakeLists.txt:90 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/razers3/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/razers3 -- Found BZip2: /usr/lib64/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers3/CMakeLists.txt:112 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers3/CMakeLists.txt:113 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/rep_sep/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/rep_sep -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Deprecation Warning at apps/sak/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/sak -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sak/CMakeLists.txt:86 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/sam2matrix/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/sam2matrix -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sam2matrix/CMakeLists.txt:74 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/samcat/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/samcat -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/samcat/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/searchjoin/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/searchjoin -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/searchjoin/CMakeLists.txt:79 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/seqan_tcoffee/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/seqan_tcoffee -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/seqan_tcoffee/CMakeLists.txt:73 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/seqcons2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/seqcons2 -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/seqcons2/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/sgip/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/sgip -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sgip/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/snp_store/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/snp_store -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/snp_store/CMakeLists.txt:89 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/splazers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/splazers -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/splazers/CMakeLists.txt:87 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/stellar/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/stellar -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/stellar/CMakeLists.txt:79 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/tree_recon/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/tree_recon -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/tree_recon/CMakeLists.txt:73 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/yara/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/yara -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/yara/CMakeLists.txt:150 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (1.5s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SPHINX_EXECUTABLE SPHINX_MAN_OUTPUT SPHINX_TEXT_OUTPUT -- Build files have been written to: /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release + make -O -j1 /usr/bin/cmake -S/builddir/build/BUILD/seqan-seqan-v2.4.0 -B/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles/seqan_library.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'CMakeFiles/seqan_library.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 0%] Built target seqan_library make -f apps/alf/CMakeFiles/alf.dir/build.make apps/alf/CMakeFiles/alf.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/alf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/alf/CMakeFiles/alf.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/alf/CMakeFiles/alf.dir/build.make apps/alf/CMakeFiles/alf.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 0%] Building CXX object apps/alf/CMakeFiles/alf.dir/alf.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/alf && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/alf/CMakeFiles/alf.dir/alf.cpp.o -MF CMakeFiles/alf.dir/alf.cpp.o.d -o CMakeFiles/alf.dir/alf.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/statistics.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/alignment_free.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/alignment_free.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/alignment_free/af_n2.h: In instantiation of ‘void seqan::_alignmentFreeComparison(Matrix&, const TStringSet&, const AFScore >&) [with TValue = double; TStringSet = StringSet, Alloc<> > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/alignment_free/alignment_free_comparison.h:101:29: required from ‘void seqan::alignmentFreeComparison(Matrix&, const TStringSet&, const TComparisonMethod&) [with TStringSet = StringSet, Alloc<> > >; TValue = double; TComparisonMethod = AFScore >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 101 | _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:188:32: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 188 | alignmentFreeComparison(myMatrix, mySequenceSet, myScoreN2); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/alignment_free/af_n2.h:189:64: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 189 | itStandardisedKmerCounts = begin(standardisedKmerCounts); | ^ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 0%] Linking CXX executable ../../bin/alf cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/alf && /usr/bin/cmake -E cmake_link_script CMakeFiles/alf.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/alf.dir/alf.cpp.o -o ../../bin/alf -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 0%] Built target alf make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools/CMakeFiles/bisar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 0%] Building CXX object apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o -MF CMakeFiles/bisar.dir/bisar.cpp.o.d -o CMakeFiles/bisar.dir/bisar.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar_score.h:28:57: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 28 | struct FunctorDna5OrdValueComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:117:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:157:26: required from ‘int reAlign4(TReadGaps&, TContigGaps&, TFragmentStore&, TId&, TBsScoreCTLeft&, TBsScoreCTRight&, TBsScoreGALeft&, TBsScoreGARight&, TOptions&) [with TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TFragmentStore = seqan::FragmentStore; TId = unsigned int; TBsScoreCTLeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreCTRight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGALeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGARight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 157 | else if (*itR == *itC || (*itR == 'T' && *itC == 'C')) ++matches; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:1168:17: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1168 | reAlign4(readGaps, contigGaps, store, id, scoringSchemeCTLeft, scoringSchemeCTRight, scoringSchemeGALeft, scoringSchemeGARight, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:87, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:157:26: required from ‘int reAlign4(TReadGaps&, TContigGaps&, TFragmentStore&, TId&, TBsScoreCTLeft&, TBsScoreCTRight&, TBsScoreGALeft&, TBsScoreGARight&, TOptions&) [with TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TFragmentStore = seqan::FragmentStore; TId = unsigned int; TBsScoreCTLeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreCTRight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGALeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGARight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 157 | else if (*itR == *itC || (*itR == 'T' && *itC == 'C')) ++matches; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:1168:17: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1168 | reAlign4(readGaps, contigGaps, store, id, scoringSchemeCTLeft, scoringSchemeCTRight, scoringSchemeGALeft, scoringSchemeGARight, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar_base.h:21:14: required from ‘bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 21 | if (!open(seqFileIn, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:996:27: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 996 | loadReadsCroppedId(store, options.readFileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar_base.h:21:14: required from ‘bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 21 | if (!open(seqFileIn, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:996:27: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | loadReadsCroppedId(store, options.readFileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar_base.h:21:14: required from ‘bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 21 | if (!open(seqFileIn, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:996:27: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | loadReadsCroppedId(store, options.readFileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar_base.h:21:14: required from ‘bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 21 | if (!open(seqFileIn, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:996:27: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | loadReadsCroppedId(store, options.readFileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar_base.h:21:14: required from ‘bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 21 | if (!open(seqFileIn, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:996:27: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | loadReadsCroppedId(store, options.readFileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 1%] Linking CXX executable ../../bin/bisar cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/bisar.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/bisar.dir/bisar.cpp.o -o ../../bin/bisar -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 1%] Built target bisar make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools/CMakeFiles/casbar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 1%] Building CXX object apps/bs_tools/CMakeFiles/casbar.dir/casbar.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/bs_tools/CMakeFiles/casbar.dir/casbar.cpp.o -MF CMakeFiles/casbar.dir/casbar.cpp.o.d -o CMakeFiles/casbar.dir/casbar.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:41: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:88:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 88 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:99:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:6, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_score.h:42:57: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct FunctorDna5OrdValueComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:17:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 17 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:66:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 66 | struct LessPosLen : public ::std::binary_function < TPosLen, TPosLen, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:81:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 81 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:129:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 129 | struct LessId : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:142:37: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 142 | struct LessGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:165:40: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 165 | struct LessGPosEnd : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:184:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 184 | struct LessGPosEndOa : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:206:36: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct HigherQ : public ::std::binary_function < TQual, TQual, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:873:31: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 873 | seqan::VcfFileOut vcfFileOut(toCString(tempFileNameVcf)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bed_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:899:31: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 899 | seqan::BedFileOut bedFileOut(toCString(tempFileNameBed)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1618:57: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1618 | TContigIterator cit = begin(contigGaps, Standard()) + (_min(alignedRead.beginPos, alignedRead.endPos) + beginPosition(readGaps)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1163:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1163 | printAlignment(std::cout, layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:35: required from ‘bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1355:36: required from ‘void doSnpAndMethCalling(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, bool, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1355 | TContigGapIter refIt = iter(referenceGaps,candidateViewPos-refStart); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:755:36: required from ‘bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 755 | doSnpAndMethCalling(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, false, vcfFileOut, bedFileOut, methOptions, options); //bs /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig; TFileNames = StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:792:16: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 792 | loadContigs(fragmentStore1, genomeFileNameList); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:32: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1163:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1163 | printAlignment(std::cout, layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:35: required from ‘bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:87, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:55: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1163:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1163 | printAlignment(std::cout, layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:35: required from ‘bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig; TFileNames = StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:792:16: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 792 | loadContigs(fragmentStore1, genomeFileNameList); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:32: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1163:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1163 | printAlignment(std::cout, layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:35: required from ‘bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:55: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1163:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1163 | printAlignment(std::cout, layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:35: required from ‘bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig; TFileNames = StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:792:16: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 792 | loadContigs(fragmentStore1, genomeFileNameList); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig; TFileNames = StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:792:16: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 792 | loadContigs(fragmentStore1, genomeFileNameList); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig; TFileNames = StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:792:16: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 792 | loadContigs(fragmentStore1, genomeFileNameList); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘readMatchesFromSamBam, seqan::Alloc >, seqan::Alloc >, seqan::FormattedFile, seqan::Tag, void>, seqan::FragmentStore >, int, long, SNPCallingOptions>(seqan::String, seqan::Alloc >, seqan::Alloc >&, seqan::FormattedFile, seqan::Tag, void>&, seqan::BamAlignmentRecord&, seqan::FragmentStore >&, seqan::FragmentStore >&, int, long, long, SNPCallingOptions&)int’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:554:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘readMatchesFromSamBam, seqan::Alloc >, seqan::Alloc >, seqan::FormattedFile, seqan::Tag, void>, seqan::FragmentStore >, int, long, SNPCallingOptions>(seqan::String, seqan::Alloc >, seqan::Alloc >&, seqan::FormattedFile, seqan::Tag, void>&, seqan::BamAlignmentRecord&, seqan::FragmentStore >&, seqan::FragmentStore >&, int, long, long, SNPCallingOptions&)int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘readMatchesFromSamBam, seqan::Alloc >, seqan::Alloc >, seqan::FormattedFile, seqan::Tag, void>, seqan::FragmentStore >, int, long, SNPCallingOptions>(seqan::String, seqan::Alloc >, seqan::Alloc >&, seqan::FormattedFile, seqan::Tag, void>&, seqan::BamAlignmentRecord&, seqan::FragmentStore >&, seqan::FragmentStore >&, int, long, long, SNPCallingOptions&)int’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:554:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘readMatchesFromSamBam, seqan::Alloc >, seqan::Alloc >, seqan::FormattedFile, seqan::Tag, void>, seqan::FragmentStore >, int, long, SNPCallingOptions>(seqan::String, seqan::Alloc >, seqan::Alloc >&, seqan::FormattedFile, seqan::Tag, void>&, seqan::BamAlignmentRecord&, seqan::FragmentStore >&, seqan::FragmentStore >&, int, long, long, SNPCallingOptions&)int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘readMatchesFromSamBam, seqan::Alloc >, seqan::Alloc >, seqan::FormattedFile, seqan::Tag, void>, seqan::FragmentStore >, int, long, SNPCallingOptions>(seqan::String, seqan::Alloc >, seqan::Alloc >&, seqan::FormattedFile, seqan::Tag, void>&, seqan::BamAlignmentRecord&, seqan::FragmentStore >&, seqan::FragmentStore >&, int, long, long, SNPCallingOptions&)int’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:554:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘readMatchesFromSamBam, seqan::Alloc >, seqan::Alloc >, seqan::FormattedFile, seqan::Tag, void>, seqan::FragmentStore >, int, long, SNPCallingOptions>(seqan::String, seqan::Alloc >, seqan::Alloc >&, seqan::FormattedFile, seqan::Tag, void>&, seqan::BamAlignmentRecord&, seqan::FragmentStore >&, seqan::FragmentStore >&, int, long, long, SNPCallingOptions&)int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 3%] Linking CXX executable ../../bin/casbar cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/casbar.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/casbar.dir/casbar.cpp.o -o ../../bin/casbar -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:300:15, inlined from ‘__ct ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:87:23, inlined from ‘__ct_base ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:358:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:276:32, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:300:15, inlined from ‘__ct ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:87:23, inlined from ‘__ct_base ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:358:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:351:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:352:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:353:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:354:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:361:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:362:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:363:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:364:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:351:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:352:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:353:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:354:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:361:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:362:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:363:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:364:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 3%] Built target casbar make -f apps/bs_tools/CMakeFiles/four2three.dir/build.make apps/bs_tools/CMakeFiles/four2three.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools/CMakeFiles/four2three.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/bs_tools/CMakeFiles/four2three.dir/build.make apps/bs_tools/CMakeFiles/four2three.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Building CXX object apps/bs_tools/CMakeFiles/four2three.dir/four2three.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/bs_tools/CMakeFiles/four2three.dir/four2three.cpp.o -MF CMakeFiles/four2three.dir/four2three.cpp.o.d -o CMakeFiles/four2three.dir/four2three.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:14:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 14 | struct ConvertCT : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:23:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 23 | struct ConvertGA : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:117:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:41:23: required from ‘bool preProcess(TOptions&) [with TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | seqan::SeqFileIn seqFileIn(toCString(options.inputFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:15: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | preProcess(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:41:23: required from ‘bool preProcess(TOptions&) [with TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 41 | seqan::SeqFileIn seqFileIn(toCString(options.inputFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:15: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 146 | preProcess(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:41:23: required from ‘bool preProcess(TOptions&) [with TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | seqan::SeqFileIn seqFileIn(toCString(options.inputFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:15: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | preProcess(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:42:23: required from ‘bool preProcess(TOptions&) [with TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 42 | seqan::SeqFileOut seqFileOut(toCString(options.outputFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:15: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | preProcess(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:41:23: required from ‘bool preProcess(TOptions&) [with TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | seqan::SeqFileIn seqFileIn(toCString(options.inputFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:15: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | preProcess(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 4%] Linking CXX executable ../../bin/four2three cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/four2three.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/four2three.dir/four2three.cpp.o -o ../../bin/four2three -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Built target four2three make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/dfi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Building CXX object apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/dfi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o -MF CMakeFiles/dfi.dir/dfi.cpp.o.d -o CMakeFiles/dfi.dir/dfi.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:27: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:268:34: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct LessSubstringEnd : public binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:292:27: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 292 | struct LessRange : public binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:309:25: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 309 | struct LessLex : public binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 4%] Linking CXX executable ../../bin/dfi cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/dfi && /usr/bin/cmake -E cmake_link_script CMakeFiles/dfi.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/dfi.dir/dfi.cpp.o -o ../../bin/dfi -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:915:22: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_goUp’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Built target dfi make -f apps/fiona/CMakeFiles/compute_gain.dir/build.make apps/fiona/CMakeFiles/compute_gain.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona/CMakeFiles/compute_gain.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/fiona/CMakeFiles/compute_gain.dir/build.make apps/fiona/CMakeFiles/compute_gain.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Building CXX object apps/fiona/CMakeFiles/compute_gain.dir/compute_gain.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fiona/CMakeFiles/compute_gain.dir/compute_gain.cpp.o -MF CMakeFiles/compute_gain.dir/compute_gain.cpp.o.d -o CMakeFiles/compute_gain.dir/compute_gain.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:2: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:907:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 907 | success = open(inPostFastq, toCString(options.pathFastaFastqPostCorrection)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:907:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 907 | success = open(inPostFastq, toCString(options.pathFastaFastqPostCorrection)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:907:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 907 | success = open(inPostFastq, toCString(options.pathFastaFastqPostCorrection)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:907:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 907 | success = open(inPostFastq, toCString(options.pathFastaFastqPostCorrection)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:907:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 907 | success = open(inPostFastq, toCString(options.pathFastaFastqPostCorrection)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = Stats*; TParam = Stats]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Stats*; TParam = Stats]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = Stats*; TSource1 = Stats*; TSource2 = Stats*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = Stats]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = Stats]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Stats; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Stats; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1697 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1725 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Stats; TSpec = Alloc<>; TSize = int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1785 | return _Resize_String >::resize_(me, new_length); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = String&; TSize = int; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1149 | return resize(std::forward(me), new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:986:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 986 | resize(stats, options.numThreads); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:98:8: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> > >::Align(const seqan::Align, seqan::Alloc<> > >&)’ is deprecated [-Wdeprecated-copy] 98 | struct Stats | ^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:97: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> > >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:98:8: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> > >::Align(const seqan::Align, seqan::Alloc<> > >&)’ is deprecated [-Wdeprecated-copy] 98 | struct Stats | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> > >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:6: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘Stats::Stats(Stats&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 6%] Linking CXX executable ../../bin/compute_gain cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona && /usr/bin/cmake -E cmake_link_script CMakeFiles/compute_gain.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/compute_gain.dir/compute_gain.cpp.o -o ../../bin/compute_gain -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 6%] Built target compute_gain make -f apps/fiona/CMakeFiles/fiona.dir/build.make apps/fiona/CMakeFiles/fiona.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona/CMakeFiles/fiona.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/fiona/CMakeFiles/fiona.dir/build.make apps/fiona/CMakeFiles/fiona.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 7%] Building CXX object apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o -MF CMakeFiles/fiona.dir/fiona.cpp.o.d -o CMakeFiles/fiona.dir/fiona.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/parallel/base.h:36, from /usr/include/c++/14/parallel/algobase.h:40, from /usr/include/c++/14/parallel/algorithm:36, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:81: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:118: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:1636:34: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1636 | struct LessOverlap : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:1654:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1654 | struct LessPositionOverlap : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp: In function ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4410:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4410 | if (options.verbosity >= 1) | ^~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 82 | #define SEQAN_PROTIMESTART(a) _proFloat a = sysTime() | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4412:9: note: in expansion of macro ‘SEQAN_PROTIMESTART’ 4412 | SEQAN_PROTIMESTART(search); | ^~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:115: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4635:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4635 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:138: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:142: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3574:32: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 3574 | appendValue(correctCandidates, getOccurrences(iterSibling)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3582:24: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3582 | appendValue(correctCandidates, thickestBranchOccs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4635:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4635 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4635:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4635 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2259:22: required from ‘void seqan::goNextImpl(Iter > > >&, VSTreeIteratorTraits) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = Preorder; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2259 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1660:19: required from ‘void seqan::goNext(Iter >&, TTraits) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >; TTraits = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1660 | goNextImpl(it, traits); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1655:15: required from ‘void seqan::goNext(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1655 | goNext(it, typename GetVSTreeIteratorTraits< Iter > >::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3475:19: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3475 | goNext(iter); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >*>, seqan::InfixSegment>*; TParam = seqan::Segment >*>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >*>, InfixSegment>*; TParam = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3574:32: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 3574 | appendValue(correctCandidates, getOccurrences(iterSibling)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >*>, seqan::InfixSegment>*; TParam = seqan::Segment >*>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >*>, InfixSegment>*; TParam = Segment >*>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3582:24: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3582 | appendValue(correctCandidates, thickestBranchOccs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5002:23: required from ‘int writeOutput(unsigned int&, const TFragmentStore&, const FionaOptions&) [with TFragmentStore = seqan::FragmentStore]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5002 | success = open(outFile, toCString(options.outputFilename)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5611:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5611 | int res = writeOutput(numCorrected, store, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 302 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:320:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ [ 7%] Linking CXX executable ../../bin/fiona cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona && /usr/bin/cmake -E cmake_link_script CMakeFiles/fiona.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/fiona.dir/fiona.cpp.o -o ../../bin/fiona -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:617:18: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_goUp’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘operator++.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:345:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:280:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:290:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:617:18, inlined from ‘goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2066:18, inlined from ‘goNextImpl.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2257:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘goNextImpl.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:617:18, inlined from ‘goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2066:18, inlined from ‘goNextRightImpl.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2272:24: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘goNextRightImpl.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign.constprop.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘assign.constprop.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 7%] Built target fiona make -f apps/fiona/CMakeFiles/fiona_illumina.dir/build.make apps/fiona/CMakeFiles/fiona_illumina.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona/CMakeFiles/fiona_illumina.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/fiona/CMakeFiles/fiona_illumina.dir/build.make apps/fiona/CMakeFiles/fiona_illumina.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 9%] Building CXX object apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona && /usr/bin/g++ -DFIONA_ILLUMINA -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o -MF CMakeFiles/fiona_illumina.dir/fiona.cpp.o.d -o CMakeFiles/fiona_illumina.dir/fiona.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/parallel/base.h:36, from /usr/include/c++/14/parallel/algobase.h:40, from /usr/include/c++/14/parallel/algorithm:36, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:81: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:118: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:1636:34: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1636 | struct LessOverlap : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:1654:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1654 | struct LessPositionOverlap : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp: In function ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4410:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4410 | if (options.verbosity >= 1) | ^~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 82 | #define SEQAN_PROTIMESTART(a) _proFloat a = sysTime() | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4412:9: note: in expansion of macro ‘SEQAN_PROTIMESTART’ 4412 | SEQAN_PROTIMESTART(search); | ^~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:115: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4635:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4635 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:138: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:142: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3574:32: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 3574 | appendValue(correctCandidates, getOccurrences(iterSibling)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3582:24: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3582 | appendValue(correctCandidates, thickestBranchOccs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4635:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4635 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4635:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4635 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2259:22: required from ‘void seqan::goNextImpl(Iter > > >&, VSTreeIteratorTraits) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = Preorder; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2259 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1660:19: required from ‘void seqan::goNext(Iter >&, TTraits) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >; TTraits = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1660 | goNextImpl(it, traits); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1655:15: required from ‘void seqan::goNext(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1655 | goNext(it, typename GetVSTreeIteratorTraits< Iter > >::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3475:19: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3475 | goNext(iter); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >*>, seqan::InfixSegment>*; TParam = seqan::Segment >*>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >*>, InfixSegment>*; TParam = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3574:32: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 3574 | appendValue(correctCandidates, getOccurrences(iterSibling)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >*>, seqan::InfixSegment>*; TParam = seqan::Segment >*>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >*>, InfixSegment>*; TParam = Segment >*>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3582:24: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3582 | appendValue(correctCandidates, thickestBranchOccs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5002:23: required from ‘int writeOutput(unsigned int&, const TFragmentStore&, const FionaOptions&) [with TFragmentStore = seqan::FragmentStore]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5002 | success = open(outFile, toCString(options.outputFilename)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5611:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5611 | int res = writeOutput(numCorrected, store, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 302 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:320:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ [ 9%] Linking CXX executable ../../bin/fiona_illumina cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona && /usr/bin/cmake -E cmake_link_script CMakeFiles/fiona_illumina.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/fiona_illumina.dir/fiona.cpp.o -o ../../bin/fiona_illumina -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:617:18: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_goUp’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign.constprop.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘assign.constprop.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:280:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:290:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:617:18, inlined from ‘goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2066:18, inlined from ‘goNextImpl.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2257:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘goNextImpl.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:617:18, inlined from ‘goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2066:18, inlined from ‘goNextRightImpl.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2272:24: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘goNextRightImpl.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘operator++.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:345:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 9%] Built target fiona_illumina make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 10%] Building CXX object apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -MF CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o.d -o CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:254:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 254 | if (!open(bamFile, toCString(options.inBamPath))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:254:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 254 | if (!open(bamFile, toCString(options.inBamPath))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘main’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:266:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘main’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘main’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:266:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘main’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘main’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:266:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘main’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘main’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:266:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘main’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 10%] Linking CXX executable ../../bin/fx_bam_coverage cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/fx_bam_coverage.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -o ../../bin/fx_bam_coverage -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 10%] Built target fx_bam_coverage make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 12%] Building CXX object apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -MF CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o.d -o CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 12%] Linking CXX executable ../../bin/fx_fastq_stats cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/fx_fastq_stats.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -o ../../bin/fx_fastq_stats -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 12%] Built target fx_fastq_stats make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf/CMakeFiles/gustaf.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 12%] Building CXX object apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.0.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o -MF CMakeFiles/gustaf.dir/gustaf.cpp.o.d -o CMakeFiles/gustaf.dir/gustaf.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:24: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seeds.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_types.h:155:32: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 155 | struct LessPos : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_types.h:207:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 207 | struct LessLength : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parse_lm.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/create_stellarmatches_from_file.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_parse_options.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:25: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:97: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_out.h:1054:14: required from ‘bool _writeGlobalBreakpoints(seqan::String&, seqan::StringSet >&, seqan::StringSet&, const MSplazerOptions&, seqan::Vcf) [with TBreakpoint = Breakpoint, seqan::Alloc<> >, seqan::String > >; TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::Vcf = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1054 | if (!open(vcfOut, fn_vcf.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:283:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 283 | _writeGlobalBreakpoints(globalBreakpoints, databases, databaseIDs, msplazerOptions, Vcf()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 143 | if (!open(leftMates, toCString(fileNameL))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:30: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_smart_pointer.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_allocator.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagGff_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_out.h:356:14: required from ‘bool _writeGlobalBreakpoints(seqan::String&, const MSplazerOptions&, seqan::Gff) [with TBreakpoint = Breakpoint, seqan::Alloc<> >, seqan::String > >; seqan::Gff = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 356 | if (!open(gffOut, fn_gff.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:282:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 282 | _writeGlobalBreakpoints(globalBreakpoints, msplazerOptions, Gff()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 143 | if (!open(leftMates, toCString(fileNameL))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:30: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagGtf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_out.h:356:14: required from ‘bool _writeGlobalBreakpoints(seqan::String&, const MSplazerOptions&, seqan::Gff) [with TBreakpoint = Breakpoint, seqan::Alloc<> >, seqan::String > >; seqan::Gff = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 356 | if (!open(gffOut, fn_gff.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:282:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 282 | _writeGlobalBreakpoints(globalBreakpoints, msplazerOptions, Gff()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_out.h:1054:14: required from ‘bool _writeGlobalBreakpoints(seqan::String&, seqan::StringSet >&, seqan::StringSet&, const MSplazerOptions&, seqan::Vcf) [with TBreakpoint = Breakpoint, seqan::Alloc<> >, seqan::String > >; TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::Vcf = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1054 | if (!open(vcfOut, fn_vcf.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:283:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 283 | _writeGlobalBreakpoints(globalBreakpoints, databases, databaseIDs, msplazerOptions, Vcf()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 143 | if (!open(leftMates, toCString(fileNameL))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:30: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:190: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:801:19: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 801 | integrateAlign(align, localAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TVertexDescriptor&, TValue, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TVertexDescriptor = unsigned int; TValue = unsigned int; TCargo = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1532:18: required from ‘void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TValue, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = unsigned int; TCargo = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1532 | findIntervals(result, g, pm, act_knot, query_begin, query_end); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1513:18: required from ‘void seqan::findIntervals(String&, const IntervalTree&, TValue2, TValue2) [with TValue = unsigned int; TCargo = unsigned int; TValue2 = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1513 | findIntervals(result, tree.g, tree.pm, query_begin, query_end); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:255:18: required from ‘bool _checkRightMateMatches(const TMatch&, const seqan::String&, const TMSplazerChain&, const MSplazerOptions&) [with TMatch = StellarMatch, seqan::Alloc<> >, seqan::String > >; TMSplazerChain = MSplazerChain >, unsigned int, seqan::String, SparsePropertyMap, seqan::Alloc<> >, seqan::String > >, unsigned int>, seqan::String, seqan::Alloc<> >, seqan::String > >, seqan::Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 255 | findIntervals(confMateMatches, gustafChain.rightMateTree, mateIntervalBegin, mateIntervalEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:294:42: required from ‘bool _checkMateMatches(const TMatch&, const seqan::String&, const TMSplazerChain&, const MSplazerOptions&) [with TMatch = StellarMatch, seqan::Alloc<> >, seqan::String > >; TMSplazerChain = MSplazerChain >, unsigned int, seqan::String, SparsePropertyMap, seqan::Alloc<> >, seqan::String > >, unsigned int>, seqan::String, seqan::Alloc<> >, seqan::String > >, seqan::Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 294 | return _checkRightMateMatches(sMatch, queryMatches, gustafChain, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:458:35: required from ‘void _initialiseGraphMatePairs(QueryMatches >&, TId&, TMSplazerChain&, const MSplazerOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TMSplazerChain = MSplazerChain >, unsigned int, seqan::String, SparsePropertyMap, seqan::Alloc<> >, seqan::String > >, unsigned int>, seqan::String, seqan::Alloc<> >, seqan::String > >, seqan::Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | if (!_checkMateMatches(queryMatches.matches[i], queryMatches.matches, chain, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_algorithms.h:840:42: required from ‘void _chainQueryMatches(seqan::StringSet > >&, seqan::String&, seqan::String&, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&, const MSplazerOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TScoreAlloc = seqan::String; TMSplazerChain = MSplazerChain >, unsigned int, seqan::String, SparsePropertyMap, seqan::Alloc<> >, seqan::String > >, unsigned int>, seqan::String, seqan::Alloc<> >, seqan::String > >, seqan::Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 840 | _initialiseGraphMatePairs(stellarMatches[i], queryIds[i], chain, msplazerOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:230:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 230 | _chainQueryMatches(stellarMatches, distanceScores, queryChains, queryIDs, queries, readJoinPositions, msplazerOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1562:18: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1562 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1575:23: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1575 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1598:27: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1598 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 143 | if (!open(leftMates, toCString(fileNameL))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:30: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 143 | if (!open(leftMates, toCString(fileNameL))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:30: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 143 | if (!open(leftMates, toCString(fileNameL))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:30: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_array.h:427:10: required from ‘void seqan::assignSource(Gaps >&, const TSequence2&) [with TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequence2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 427 | value(gaps._source) = source; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:697:26: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | _fillMatrixBestEndsLeft(matrixLeft, possibleEndsLeft, infH, infV, seed, seedOld, scoreMatrix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:852:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 852 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:697:26: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | _fillMatrixBestEndsLeft(matrixLeft, possibleEndsLeft, infH, infV, seed, seedOld, scoreMatrix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:852:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 852 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:697:26: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | _fillMatrixBestEndsLeft(matrixLeft, possibleEndsLeft, infH, infV, seed, seedOld, scoreMatrix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:852:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 852 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned long’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const long unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned long const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 14%] Linking CXX executable ../../bin/gustaf cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gustaf.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/gustaf.dir/gustaf.cpp.o -o ../../bin/gustaf -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘_getNextBestEndPosition’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_waterman_eggert_impl.h:659:20, inlined from ‘_localAlignmentNext’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:572:42, inlined from ‘nextLocalAlignment’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35, inlined from ‘nextLocalAlignment’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30, inlined from ‘verifySwiftHit’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:607:30, inlined from ‘stellar.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘stellar.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:915:22, inlined from ‘_goDown’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:814:22, inlined from ‘goDown’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20, inlined from ‘goNextImpl’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2256:24, inlined from ‘goNext’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1660:19, inlined from ‘goNext’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1655:15, inlined from ‘findRepeats’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:527:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘findRepeats’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:915:22, inlined from ‘goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2066:18, inlined from ‘goNextImpl’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2257:28, inlined from ‘goNext’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1660:19, inlined from ‘goNext’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1655:15, inlined from ‘findRepeats’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:527:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘findRepeats’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:300:15, inlined from ‘__ct ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:87:23, inlined from ‘__ct_base ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer.h:328:8: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:276:32, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:300:15, inlined from ‘__ct ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:87:23, inlined from ‘__ct_base ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer.h:328:8: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘pop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:276:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 14%] Built target gustaf make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 14%] Building CXX object apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.0.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -MF CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o.d -o CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 257 | _open(*this, fileName, openMode, True()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 196 | seqan::SeqFileIn l(toCString(fileNameL)); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:25: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 196 | seqan::SeqFileIn l(toCString(fileNameL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:25: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 196 | seqan::SeqFileIn l(toCString(fileNameL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:25: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 196 | seqan::SeqFileIn l(toCString(fileNameL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:25: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:330:27: required from ‘int _writeSequences(seqan::CharString&, const seqan::StringSet >&, const seqan::StringSet > >&, const seqan::StringSet > >&) [with TSequence = seqan::String, seqan::Alloc<> >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 330 | seqan::SeqFileOut seqFile(toCString(outPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:439:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 439 | _writeSequences(options.outPaths[0], seqs, sIds, quals); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 196 | seqan::SeqFileIn l(toCString(fileNameL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:25: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:330:27: required from ‘int _writeSequences(seqan::CharString&, const seqan::StringSet >&, const seqan::StringSet > >&, const seqan::StringSet > >&) [with TSequence = seqan::String, seqan::Alloc<> >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 330 | seqan::SeqFileOut seqFile(toCString(outPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:439:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 439 | _writeSequences(options.outPaths[0], seqs, sIds, quals); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 15%] Linking CXX executable ../../bin/gustaf_mate_joining cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gustaf_mate_joining.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -o ../../bin/gustaf_mate_joining -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 15%] Built target gustaf_mate_joining make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/insegt /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 15%] Building CXX object apps/insegt/CMakeFiles/insegt.dir/insegt.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/insegt && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/insegt/CMakeFiles/insegt.dir/insegt.cpp.o -MF CMakeFiles/insegt.dir/insegt.cpp.o.d -o CMakeFiles/insegt.dir/insegt.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:16: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:20: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h: In instantiation of ‘void seqan::createReadCountGFF(TFile&, TReadAnnoStore&, FragmentStore&) [with TFile = std::basic_fstream; TReadAnnoStore = String >; TSpec = void; TConfig = FragmentStoreConfig]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:889:23: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 889 | createReadCountGFF(readOutput, readAnnoStore, fragStore); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 199 | ngsOverlapper(options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:75:35: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 75 | itAnnoIds = begin(getValue(itCountStore).annoIds); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:12: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:76:38: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 76 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:100:43: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 100 | itAnnoIds = begin(getValue(itCountStore).annoIds); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:101:46: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 101 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:134:51: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 134 | itAnnoIds = begin(getValue(itCountStore).annoIds); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:135:54: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 135 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:169:43: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 169 | itAnnoIds = begin(getValue(itCountStore).annoIds); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:170:46: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 170 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h: In instantiation of ‘seqan::Iter > seqan::nodeDown(const Iter >&) [with TFragmentStore = FragmentStore<>; TSpec = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:48:64: required from ‘void seqan::adjustParentEntries(FragmentStore&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 48 | getAnnotation(it).contigId = getAnnotation(nodeDown(it)).contigId; // If no child exists: nothing happens /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:851:21: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 851 | adjustParentEntries(fragStore); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:853:50: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)’ is deprecated [-Wdeprecated-copy] 853 | Iter > tmp(it); | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: because ‘seqan::Iter, seqan::AnnotationTree<> >’ has user-provided ‘const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]’ 272 | operator = (Iter const &_origin) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:855:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)’ is deprecated [-Wdeprecated-copy] 855 | return tmp; | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: because ‘seqan::Iter, seqan::AnnotationTree<> >’ has user-provided ‘const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]’ 272 | operator = (Iter const &_origin) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:22: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h: In instantiation of ‘void seqan::getIdsForRead(TAnnoIds&, FragmentStore&, TIntervalTree&, TIntervals&, unsigned int) [with TAnnoIds = StringSet >, Owner<> >; TSpec = void; TConfig = FragmentStoreConfig; TIntervalTree = IntervalTree; TIntervals = String, Alloc<> >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:754:18: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: 754 | getIdsForRead(ids, fragStore, *intervalTree, getValue(it).intervals, offsetInterval); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:90:13: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 90 | itR = begin(ids); | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h: In instantiation of ‘void seqan::buildAnnoCountStore(TAnnoCountStore&, FragmentStore&, TReadAnnoStore&) [with TAnnoCountStore = String >; TSpec = void; TConfig = FragmentStoreConfig; TReadAnnoStore = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:760:21: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 760 | buildAnnoCountStore(annoCountStore, fragStore, readAnnoStore); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:536:51: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 536 | itAnnoIds = begin(getValue(itRead).annoIds); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:537:54: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 537 | itAnnoIdsEnd = end(getValue(itRead).annoIds); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h: In instantiation of ‘void seqan::buildTupleCountStore_Fusion(TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig; TReadAnnoStore = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:761:29: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 761 | buildTupleCountStore_Fusion(tupleCountStore, tupleCountStore_Fusion, fragStore, readAnnoStore, tupelSize, exact_nTuple); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:191:92: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 191 | itSecTuple = begin(tempSecTupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:192:95: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 192 | itSecTupleEnd = end(tempSecTupleSet); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:208:57: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 208 | itTuple = begin(tupleSet); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:209:60: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 209 | itTupleEnd = end(tupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:238:76: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 238 | itSecTuple = begin(secTupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:239:79: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 239 | itSecTupleEnd = end(secTupleSet); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:291:57: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 291 | itTuple = begin(tupleSet); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:292:60: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 292 | itTupleEnd = end(tupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:298:68: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 298 | itSecTuple = begin(secTupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:299:71: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 299 | itSecTupleEnd = end(secTupleSet); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h: In instantiation of ‘void seqan::buildTupleCountStore(TTupleCountStore&, FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = String >; TSpec = void; TConfig = FragmentStoreConfig; TReadAnnoStore = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:624:22: required from ‘void seqan::getResults(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 624 | buildTupleCountStore(tupleCountStore, fragStore, readAnnoStore, tupelSize, exact_nTuple); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:872:13: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 872 | getResults(readAnnoStore, annoCountStore, tupleCountStore, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:354:57: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 354 | itTuple = begin(tupleSet); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:355:60: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 355 | itTupleEnd = end(tupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:384:76: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 384 | itSecTuple = begin(secTupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:385:79: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 385 | itSecTupleEnd = end(secTupleSet); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:838:15: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 838 | BamFileIn inSam(toCString(options.nameSAM)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/base.h: In instantiation of ‘void seqan::create_nTuple(TStringSet&, FragmentStore&, const TStringSet&, const TId&, const unsigned int&) [with TStringSet = StringSet >, Owner<> >; TSpec = void; TConfig = FragmentStoreConfig; TId = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:122:60: required from ‘void seqan::buildTupleCountStore_Fusion(TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig; TReadAnnoStore = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 122 | if (exact_nTuple && n <= length(annoIds)) create_nTuple(tupleSet, fragStore, annoIds, getValue(itP), n); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:761:29: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 761 | buildTupleCountStore_Fusion(tupleCountStore, tupleCountStore_Fusion, fragStore, readAnnoStore, tupelSize, exact_nTuple); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/base.h:69:23: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 69 | itSet = begin(tempTupleSet); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/base.h:70:26: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 70 | itSetEnd = end(tempTupleSet); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/base.h: In instantiation of ‘void seqan::create_Tuple(TStringSet&, FragmentStore&, const TStringSet&, const TId&, const unsigned int&) [with TStringSet = StringSet >, Owner<> >; TSpec = void; TConfig = FragmentStoreConfig; TId = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:126:41: required from ‘void seqan::buildTupleCountStore_Fusion(TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig; TReadAnnoStore = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 126 | else if (!exact_nTuple) create_Tuple(tupleSet, fragStore, annoIds, getValue(itP), n); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:761:29: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 761 | buildTupleCountStore_Fusion(tupleCountStore, tupleCountStore_Fusion, fragStore, readAnnoStore, tupelSize, exact_nTuple); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/base.h:97:20: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 97 | it = begin(tempTupleSet); | ~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/base.h:98:23: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 98 | itEnd = end(tempTupleSet); | ~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagGff_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:848:15: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 848 | GffFileIn inGff(toCString(options.nameGFF)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = unsigned int; TCargo = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_intervaltree.h:182:18: required from ‘void seqan::findIntervalsForInterval(String&, TIntervalTree&, TInterval&, unsigned int) [with TIntervalTree = IntervalTree; TInterval = Interval; TCargo = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 182 | findIntervals(result1, intervalTree.g, intervalTree.pm, interval.i1 + offsetInterval); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:85:27: required from ‘void seqan::getIdsForRead(TAnnoIds&, FragmentStore&, TIntervalTree&, TIntervals&, unsigned int) [with TAnnoIds = StringSet >, Owner<> >; TSpec = void; TConfig = FragmentStoreConfig; TIntervalTree = IntervalTree; TIntervals = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 85 | findIntervalsForInterval(value(itR), intervalTree, getValue(itI), offsetInterval); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:754:18: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 754 | getIdsForRead(ids, fragStore, *intervalTree, getValue(it).intervals, offsetInterval); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1441 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1453 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1475 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:838:15: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 838 | BamFileIn inSam(toCString(options.nameSAM)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagGtf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:848:15: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 848 | GffFileIn inGff(toCString(options.nameGFF)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = Segment, Alloc<> >, InfixSegment>; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 466 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2236:27: required from ‘void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = AlignedReadStoreElement, void>*; TPos = long int; TSize = long int; TReadSeqStore = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2236 | insertGaps(gaps, insPos - rBegin, blkLen); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2321:40: required from ‘void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = Gaps, AnchorGaps, Alloc<> > > >; TContigGapsPW = Gaps, AnchorGaps, Alloc<> >, InfixSegment> > >; TReadGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TAlignedReadIter = AlignedReadStoreElement, void>*; TReadSeqStore = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2321 | _alignedReadsInsertGaps(overlappingAlignedReadsBegin1, overlappingAlignedReadsEnd1, insPos, blkLen, readSeqStore); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2437:31: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2437 | _twoWayMergeAlignments( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^ 2438 | contigGapsGlobal, contigGapsPW, readGaps, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2439 | firstOverlapOld, lastOverlapOld, firstOverlapNew, it, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2440 | store.readSeqStore); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:337:41: required from ‘void seqan::readRecords(FragmentStore&, BamIOContext&, TForwardIter&, const TFormat&, const FragStoreImportFlags&) [with TSpec = void; TConfig = FragmentStoreConfig; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >; TForwardIter = Iter >, StreamIterator > >; TFormat = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 337 | convertPairWiseToGlobalAlignment(store, contigAnchorGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&, const FragStoreImportFlags&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 373 | readRecords(store, bamFile, FragStoreImportFlags()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:839:16: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 839 | readRecords(fragStore, inSam); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2393:29: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 2393 | TContigGapsPW contigGapsPW(/*contigInfix, */gaps[it->id - offsetRecord]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:337:41: required from ‘void seqan::readRecords(FragmentStore&, BamIOContext&, TForwardIter&, const TFormat&, const FragStoreImportFlags&) [with TSpec = void; TConfig = FragmentStoreConfig; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >; TForwardIter = Iter >, StreamIterator > >; TFormat = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 337 | convertPairWiseToGlobalAlignment(store, contigAnchorGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&, const FragStoreImportFlags&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 373 | readRecords(store, bamFile, FragStoreImportFlags()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:839:16: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 839 | readRecords(fragStore, inSam); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2394:29: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2394 | TReadGaps readGaps(store.readSeqStore[it->readId], it->gaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:337:41: required from ‘void seqan::readRecords(FragmentStore&, BamIOContext&, TForwardIter&, const TFormat&, const FragStoreImportFlags&) [with TSpec = void; TConfig = FragmentStoreConfig; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >; TForwardIter = Iter >, StreamIterator > >; TFormat = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 337 | convertPairWiseToGlobalAlignment(store, contigAnchorGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&, const FragStoreImportFlags&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 373 | readRecords(store, bamFile, FragStoreImportFlags()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:839:16: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 839 | readRecords(fragStore, inSam); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::Tag >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:573:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::Tag >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::Tag >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:573:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::Tag >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::Tag >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:573:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::Tag >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 17%] Linking CXX executable ../../bin/insegt cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/insegt && /usr/bin/cmake -E cmake_link_script CMakeFiles/insegt.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/insegt.dir/insegt.cpp.o -o ../../bin/insegt -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 17%] Built target insegt make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_sim.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 18%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -MF CMakeFiles/mason_sim.dir/external_split_merge.cpp.o.d -o CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:49: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:53: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:171:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In member function ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:171:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In member function ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:171:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In member function ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:171:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In member function ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 18%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -MF CMakeFiles/mason_sim.dir/genomic_variants.cpp.o.d -o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:55: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:53, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = int; TCargo = GenomicInterval]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1502:18: required from ‘void seqan::findIntervals(String&, const IntervalTree&, TValue2) [with TValue = int; TCargo = GenomicInterval; TValue2 = int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1502 | findIntervals(result, it.g, it.pm, query); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:718:18: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 718 | findIntervals(intervals, svIntervalTree, svPos); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1441 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1453 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1475 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 20%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o -MF CMakeFiles/mason_sim.dir/mason_options.cpp.o.d -o CMakeFiles/mason_sim.dir/mason_options.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:53: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 20%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -MF CMakeFiles/mason_sim.dir/methylation_levels.cpp.o.d -o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:41: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:53, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 21%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_454.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_454.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 21%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_base.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_base.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 23%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_genome.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:106:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 106 | if (!open(stream, filename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:106:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 106 | if (!open(stream, filename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:106:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 106 | if (!open(stream, filename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 23%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:264:56: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 140 | _host(std::forward(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:264:56: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:98:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 98 | class ModifiedIterator > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:193:25: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 193 | TFragIter it = begin(frag, seqan::Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:264:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 663 | TResult tmp(end(host(me), tag_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:193:25: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 193 | TFragIter it = begin(frag, seqan::Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:264:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 25%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:153:56: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 140 | _host(std::forward(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:153:56: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:98:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 98 | class ModifiedIterator > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:59:25: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 59 | TFragIter it = begin(frag, seqan::Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:153:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 663 | TResult tmp(end(host(me), tag_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:59:25: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 59 | TFragIter it = begin(frag, seqan::Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:153:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 25%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -MF CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o.d -o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:167:18: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 167 | if (!open(vcfFileIn, toCString(vcfFileName))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:167:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 167 | if (!open(vcfFileIn, toCString(vcfFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 25%] Linking CXX static library libmason_sim.a cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -P CMakeFiles/mason_sim.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_sim.dir/link.txt --verbose=1 /usr/bin/ar qc libmason_sim.a CMakeFiles/mason_sim.dir/external_split_merge.cpp.o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o CMakeFiles/mason_sim.dir/mason_options.cpp.o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o CMakeFiles/mason_sim.dir/simulate_454.cpp.o CMakeFiles/mason_sim.dir/simulate_base.cpp.o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o /usr/bin/ranlib libmason_sim.a make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 25%] Built target mason_sim make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 25%] Building CXX object apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o -MF CMakeFiles/mason_genome.dir/mason_genome.cpp.o.d -o CMakeFiles/mason_genome.dir/mason_genome.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 26%] Linking CXX executable ../../bin/mason_genome cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_genome.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_genome.dir/mason_genome.cpp.o -o ../../bin/mason_genome -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 26%] Built target mason_genome make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 28%] Building CXX object apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -MF CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o.d -o CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:143:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 143 | if (!open(outStream, toCString(options.methFastaOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:143:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 143 | if (!open(outStream, toCString(options.methFastaOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:143:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 143 | if (!open(outStream, toCString(options.methFastaOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 28%] Linking CXX executable ../../bin/mason_methylation cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_methylation.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -o ../../bin/mason_methylation -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 28%] Built target mason_methylation make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 28%] Building CXX object apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -MF CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o.d -o CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:142:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 142 | if (!open(inFragments, toCString(options.inputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:142:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 142 | if (!open(inFragments, toCString(options.inputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:142:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 142 | if (!open(inFragments, toCString(options.inputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:153:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 153 | if (!open(outReads, toCString(options.outFileNameLeft))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:142:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 142 | if (!open(inFragments, toCString(options.inputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 29%] Linking CXX executable ../../bin/mason_frag_sequencing cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_frag_sequencing.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -o ../../bin/mason_frag_sequencing -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 29%] Built target mason_frag_sequencing make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 31%] Building CXX object apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -MF CMakeFiles/mason_variator.dir/mason_variator.cpp.o.d -o CMakeFiles/mason_variator.dir/mason_variator.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/random:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:43: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:833:18: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 833 | if (!open(vcfFileOut, toCString(options.vcfOutFile))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:884:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 884 | if (!open(outSeqStream, toCString(options.fastaOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:833:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 833 | if (!open(vcfFileOut, toCString(options.vcfOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:884:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 884 | if (!open(outSeqStream, toCString(options.fastaOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:884:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 884 | if (!open(outSeqStream, toCString(options.fastaOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 31%] Linking CXX executable ../../bin/mason_variator cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_variator.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_variator.dir/mason_variator.cpp.o -o ../../bin/mason_variator -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_simulateFromSizes’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:369:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551504’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_simulateFromSizes’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 31%] Built target mason_variator make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 31%] Building CXX object apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -MF CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o.d -o CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:43: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:51: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:103:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 103 | if (!open(outStream, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:103:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 103 | if (!open(outStream, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:103:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 103 | if (!open(outStream, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 31%] Linking CXX executable ../../bin/mason_materializer cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_materializer.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -o ../../bin/mason_materializer -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 31%] Built target mason_materializer make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 32%] Building CXX object apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -MF CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o.d -o CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:51: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:1155:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1155 | if (!open(outSeqsLeft, toCString(options.outFileNameLeft))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:1155:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1155 | if (!open(outSeqsLeft, toCString(options.outFileNameLeft))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:1155:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1155 | if (!open(outSeqsLeft, toCString(options.outFileNameLeft))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:46: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_array.h:269:34: required from ‘void seqan::_reinitArrayGaps(Gaps >&) [with TSequence = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 269 | _setLength(gaps, length(value(gaps._source))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_array.h:155:25: required from ‘seqan::Gaps >::Gaps(TSequence&) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 155 | _reinitArrayGaps(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:219:57: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 219 | seqan::Gaps gapsContig(contigInfix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:45: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: required from ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 586 | return Iter >(container(left), hostIterator(left) + right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 32%] Linking CXX executable ../../bin/mason_simulator cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_simulator.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -o ../../bin/mason_simulator -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:276:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘appendOperation’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:379:22, inlined from ‘simulateRead’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:374:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551600’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘simulateRead’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘appendOperation’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:379:22, inlined from ‘simulateRead’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:379:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551600’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘simulateRead’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 32%] Built target mason_simulator make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 34%] Building CXX object apps/mason2/CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -MF CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o.d -o CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:149:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 149 | if (!open(seqFileOut, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagGff_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:152:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 152 | if (!open(gffFileIn, toCString(options.inputGffFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:149:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 149 | if (!open(seqFileOut, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagGtf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:152:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 152 | if (!open(gffFileIn, toCString(options.inputGffFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:149:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 149 | if (!open(seqFileOut, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/gff_io/gff_io_base.h:379:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/gff_io/gff_io_base.h:386:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 34%] Linking CXX executable ../../bin/mason_splicing cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_splicing.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -o ../../bin/mason_splicing -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:276:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 34%] Built target mason_splicing make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 35%] Building CXX object apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o -MF CMakeFiles/mason_tests.dir/mason_tests.cpp.o.d -o CMakeFiles/mason_tests.dir/mason_tests.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_tests.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_tests.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_tests.cpp:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 35%] Linking CXX executable ../../bin/mason_tests cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_tests.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_tests.dir/mason_tests.cpp.o -o ../../bin/mason_tests -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘addVertex’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 35%] Built target mason_tests make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers/CMakeFiles/micro_razers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 37%] Building CXX object apps/micro_razers/CMakeFiles/micro_razers.dir/micro_razers.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.0.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/micro_razers/CMakeFiles/micro_razers.dir/micro_razers.cpp.o -MF CMakeFiles/micro_razers.dir/micro_razers.cpp.o.d -o CMakeFiles/micro_razers.dir/micro_razers.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:25: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:643:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 643 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:672:49: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 672 | struct LessRNoEdistHLen : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:728:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 728 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:760:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 760 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/outputFormat.h:126:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, const TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobalHamming) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobalHamming = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1359:35: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1359 | return matchVerify(m,inf,rseqNo,readSet,options,MicroRNA()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: initializing argument 2 of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, const RazerSOptions&, MicroRNA) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TSpec = RazerSSpec<>]’ 1257 | Segment inf, // potential match genome region | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1471:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:222: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1697:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1697 | while (find(swiftFinder, swiftPattern, 0.2)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1697:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1697 | while (find(swiftFinder, swiftPattern, 0.2)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:68: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1471:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1471 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1472:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1472 | TReadRev readRev(readSet[rseqNo]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1697:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1697 | while (find(swiftFinder, swiftPattern, 0.2)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2279:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2279 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1697:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1697 | while (find(swiftFinder, swiftPattern, 0.2)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2282:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2282 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1440:15: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1440 | TMyersFinder myersFinder(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1473:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1473 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1666 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 1666 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1666 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1455:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1455 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1473:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1473 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 599 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1478:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1478 | while (find(myersFinderRev, myersPatternRev, maxScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 254 | setValue(_dataHost(me), std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1971:11: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1971 | setHost(forwardPatterns[i], indexText(swiftIndex)[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:992:51, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:1285:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:1010:66, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:1285:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:1020:53, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:1285:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 37%] Building CXX object apps/micro_razers/CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.0.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/micro_razers/CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -MF CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o.d -o CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/param_tabs.cpp [ 37%] Linking CXX executable ../../bin/micro_razers cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers && /usr/bin/cmake -E cmake_link_script CMakeFiles/micro_razers.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/micro_razers.dir/micro_razers.cpp.o CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -o ../../bin/micro_razers -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 37%] Built target micro_razers make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 39%] Building CXX object apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -MF CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o.d -o CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Roi_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:432:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 432 | if (!open(roiFileIn, toCString(options.inputFileName))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Roi_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:432:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 432 | if (!open(roiFileIn, toCString(options.inputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 39%] Linking CXX executable ../../bin/roi_plot_thumbnails cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/roi_plot_thumbnails.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -o ../../bin/roi_plot_thumbnails -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 39%] Built target roi_plot_thumbnails make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi/CMakeFiles/bam2roi.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 40%] Building CXX object apps/ngs_roi/CMakeFiles/bam2roi.dir/bam2roi.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/bam2roi.dir/bam2roi.cpp.o -MF CMakeFiles/bam2roi.dir/bam2roi.cpp.o.d -o CMakeFiles/bam2roi.dir/bam2roi.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:88:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 88 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:99:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Roi_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:318:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 318 | if (!open(roiFileOut, toCString(options.outputFileName))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Roi_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:318:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 318 | if (!open(roiFileOut, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 40%] Building CXX object apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o -MF CMakeFiles/bam2roi.dir/roi_builder.cpp.o.d -o CMakeFiles/bam2roi.dir/roi_builder.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:88:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 88 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:99:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 42%] Linking CXX executable ../../bin/bam2roi cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam2roi.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/bam2roi.dir/bam2roi.cpp.o CMakeFiles/bam2roi.dir/roi_builder.cpp.o -o ../../bin/bam2roi -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 42%] Built target bam2roi make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 43%] Building CXX object apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o -MF CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o.d -o CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:41: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Roi_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:876:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 876 | if (!open(roiFileIn, toCString(options.inputRoiFile))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Roi_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:876:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 876 | if (!open(roiFileIn, toCString(options.inputRoiFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/gff_io/gff_io_base.h:379:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/gff_io/gff_io_base.h:386:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 43%] Building CXX object apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o -MF CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o.d -o CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/gff_io.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 45%] Building CXX object apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -MF CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o.d -o CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 45%] Linking CXX executable ../../bin/roi_feature_projection cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/roi_feature_projection.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -o ../../bin/roi_feature_projection -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 45%] Built target roi_feature_projection make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Built target pair_align_global_1111 make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o -MF CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o.d -o CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Built target pair_align_lcs make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_local.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -MF CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o.d -o CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Built target pair_align_local make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 48%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 48%] Built target pair_align_global_0000 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 48%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 48%] Built target pair_align_global_0001 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Built target pair_align_global_0010 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Built target pair_align_global_0011 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 51%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 51%] Built target pair_align_global_0100 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 51%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 51%] Built target pair_align_global_0101 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Built target pair_align_global_0110 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Built target pair_align_global_0111 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Built target pair_align_global_1000 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 54%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 54%] Built target pair_align_global_1001 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 54%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 54%] Built target pair_align_global_1010 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 56%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 56%] Built target pair_align_global_1011 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 56%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 56%] Built target pair_align_global_1100 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 57%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 57%] Built target pair_align_global_1101 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 57%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 57%] Built target pair_align_global_1110 make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 59%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o -MF CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o.d -o CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 59%] Linking CXX static library libpair_align_lib.a cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/cmake -P CMakeFiles/pair_align_lib.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/pair_align_lib.dir/link.txt --verbose=1 /usr/bin/ar qc libpair_align_lib.a CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o /usr/bin/ranlib libpair_align_lib.a make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 59%] Built target pair_align_lib make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/CMakeFiles/pair_align.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 60%] Building CXX object apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o -MF CMakeFiles/pair_align.dir/pair_align.cpp.o.d -o CMakeFiles/pair_align.dir/pair_align.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 60%] Linking CXX executable ../../bin/pair_align cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align && /usr/bin/cmake -E cmake_link_script CMakeFiles/pair_align.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/pair_align.dir/pair_align.cpp.o -o ../../bin/pair_align lib/libpair_align_lib.a -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 60%] Built target pair_align make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 62%] Building CXX object apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o -MF CMakeFiles/param_chooser.dir/param_chooser.cpp.o.d -o CMakeFiles/param_chooser.dir/param_chooser.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:32: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:33, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:30, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:676:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 676 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:704:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 704 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:730:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 730 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:748:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 748 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:770:45: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 770 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1430:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:222: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1653:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2242 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1653:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2245:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2245 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:68: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1430:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1430 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1431:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1431 | TReadRev readRev(readSet[rseqNo]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1653:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2253:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2253 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1653:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2256:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2256 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1399:15: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1399 | TMyersFinder myersFinder(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1432:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1432 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1625:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1625 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2239:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1625:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 1625 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2242 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1625:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1625 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2245:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2245 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1414:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1414 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1432:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1432 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 599 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1437:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:840:14: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2047:11: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2047 | setHost(forwardPatterns[i], indexText(swiftIndex)[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2239:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:829:51, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1107:20, inlined from ‘main’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘main’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 62%] Linking CXX executable ../../bin/param_chooser cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/param_chooser.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/param_chooser.dir/param_chooser.cpp.o -o ../../bin/param_chooser -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 62%] Built target param_chooser make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 62%] Building CXX object apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -MF CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o.d -o CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:33, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:30, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:676:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 676 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:704:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 704 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:730:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 730 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:748:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 748 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:770:45: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 770 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams, std::allocator >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::__cxx11::basic_stringstream, std::allocator >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:829:51: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::parseGappedParams, std::allocator >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::__cxx11::basic_stringstream, std::allocator >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams, std::allocator >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::__cxx11::basic_stringstream, std::allocator >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:847:66: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::parseGappedParams, std::allocator >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::__cxx11::basic_stringstream, std::allocator >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams, std::allocator >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::__cxx11::basic_stringstream, std::allocator >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:857:53: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::parseGappedParams, std::allocator >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::__cxx11::basic_stringstream, std::allocator >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 64%] Linking CXX executable ../../bin/test_funcs_param_chooser cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_funcs_param_chooser.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -o ../../bin/test_funcs_param_chooser -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 64%] Built target test_funcs_param_chooser make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 64%] Building CXX object apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -MF CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o.d -o CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:27: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 65%] Linking CXX executable ../../bin/rabema_prepare_sam cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_prepare_sam.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -o ../../bin/rabema_prepare_sam -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 65%] Built target rabema_prepare_sam make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 67%] Building CXX object apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -MF CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o.d -o CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:31: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:105:10: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 105 | std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 118 | _host(_toPointer(host)), /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:254:100: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 254 | TModifiedString rRightInterval(infix(errorCurve, rightmostPos, offset + intervalLength)); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:257:52: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:257:52: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:513:97: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 513 | typename Iterator, Tag const >::Type temp_(begin(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:257:91: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h: In instantiation of ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:558:19: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 558 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:660:22: required from ‘void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 660 | _patternFirstInit(pattern, needle(pattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 255 | _reinitPattern(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from ‘void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 403 | Pattern pattern(read, -(int)length(read) * 40); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from ‘int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 899 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:1203:37: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1203 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, inBam, readNameStore, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1204 | contigNames(context(inBam)), faiIndex, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 254 | setValue(_dataHost(me), std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from ‘void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 403 | Pattern pattern(read, -(int)length(read) * 40); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from ‘int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 899 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:1203:37: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1203 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, inBam, readNameStore, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1204 | contigNames(context(inBam)), faiIndex, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:625:12: required from ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 625 | return ModifiedString(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 255 | _reinitPattern(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from ‘void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 403 | Pattern pattern(read, -(int)length(read) * 40); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from ‘int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 899 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:1203:37: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1203 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, inBam, readNameStore, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1204 | contigNames(context(inBam)), faiIndex, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 67%] Linking CXX executable ../../bin/rabema_build_gold_standard cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_build_gold_standard.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -o ../../bin/rabema_build_gold_standard -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 67%] Built target rabema_build_gold_standard make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 67%] Building CXX object apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -MF CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o.d -o CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:33: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = unsigned int; TCargo = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1502:18: required from ‘void seqan::findIntervals(String&, const IntervalTree&, TValue2) [with TValue = unsigned int; TCargo = unsigned int; TValue2 = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1502 | findIntervals(result, it.g, it.pm, query); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:644:22: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 644 | findIntervals(queryResult, intervalTrees[seqId], lastPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1003:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1401:45: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1441 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1453 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1475 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h: In instantiation of ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:558:19: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 558 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:660:22: required from ‘void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 660 | _patternFirstInit(pattern, needle(pattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 255 | _reinitPattern(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:623:51: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 623 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1003:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1401:45: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 254 | setValue(_dataHost(me), std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:623:51: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 623 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1003:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1401:45: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:625:12: required from ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 625 | return ModifiedString(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 255 | _reinitPattern(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:623:51: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 623 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1003:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1401:45: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 68%] Linking CXX executable ../../bin/rabema_evaluate cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_evaluate.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -o ../../bin/rabema_evaluate -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 68%] Built target rabema_evaluate make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 68%] Building CXX object apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o -MF CMakeFiles/rabema_do_search.dir/do_search.cpp.o.d -o CMakeFiles/rabema_do_search.dir/do_search.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:8: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:3: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:105:10: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 105 | std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 118 | _host(_toPointer(host)), /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:254:100: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 254 | TModifiedString rRightInterval(infix(errorCurve, rightmostPos, offset + intervalLength)); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:257:52: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:257:52: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:513:97: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 513 | typename Iterator, Tag const >::Type temp_(begin(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:257:91: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h: In instantiation of ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:558:19: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 558 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:660:22: required from ‘void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 660 | _patternFirstInit(pattern, needle(pattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 255 | _reinitPattern(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:27:89: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 27 | Pattern pattern(read, -static_cast(length(read))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:840:14: required from ‘void seqan::setValue(Holder >&, const TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 840 | set(value(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 254 | setValue(_dataHost(me), std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:27:89: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 27 | Pattern pattern(read, -static_cast(length(read))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:625:12: required from ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 625 | return ModifiedString(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:558:19: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 558 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:660:22: required from ‘void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 660 | _patternFirstInit(pattern, needle(pattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 255 | _reinitPattern(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:27:89: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 27 | Pattern pattern(read, -static_cast(length(read))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 70%] Linking CXX executable ../../bin/rabema_do_search cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_do_search.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_do_search.dir/do_search.cpp.o -o ../../bin/rabema_do_search -lrt -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 70%] Built target rabema_do_search make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 70%] Building CXX object apps/razers/CMakeFiles/razers.dir/razers.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers/CMakeFiles/razers.dir/razers.cpp.o -MF CMakeFiles/razers.dir/razers.cpp.o.d -o CMakeFiles/razers.dir/razers.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:28, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:696:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 696 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:728:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 728 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:760:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 760 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:51: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/outputFormat.h:126:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:221:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct LessPairErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1471:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1471:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment, Alloc<> >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = Segment, Alloc<> >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:789:10: required from ‘TStream& seqan::operator<<(TStream&, const Segment&) [with TStream = VirtualStream >; THost = const String, Alloc<> >; TSpec = InfixSegment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 789 | write(it, source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/outputFormat.h:722:12: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | file << reads[(*it).rseqNo]; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:232:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 232 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:395:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 395 | data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:394:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 394 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:222: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1699:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:68: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1699:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1471:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1471 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1472:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1472 | TReadRev readRev(readSet[rseqNo]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2279:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2279 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1699:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2279:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2279 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2282:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2282 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1699:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2282:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2282 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1876:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1876 | finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1845:48: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1965 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1473:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1473 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment, Alloc<> >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = Segment, Alloc<> >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:789:10: required from ‘TStream& seqan::operator<<(TStream&, const Segment&) [with TStream = VirtualStream >; THost = const String, Alloc<> >; TSpec = InfixSegment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 789 | write(it, source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/outputFormat.h:722:12: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | file << reads[(*it).rseqNo]; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:232:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 232 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:375:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 375 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 1666 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:375:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 375 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1666 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:375:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 375 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1666 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1455:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1455 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1473:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1473 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 369 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1845:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1965 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 599 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1478:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1478 | while (find(myersFinderRev, myersPatternRev, maxScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 254 | setValue(_dataHost(me), std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1971:11: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1971 | setHost(forwardPatterns[i], indexText(swiftIndex)[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 135 | assignValue(*this, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:259:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:394:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 394 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/paramChooser.h:992:51, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/paramChooser.h:1285:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/paramChooser.h:1010:66, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/paramChooser.h:1285:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/paramChooser.h:1020:53, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/paramChooser.h:1285:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 71%] Building CXX object apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o -MF CMakeFiles/razers.dir/param_tabs.cpp.o.d -o CMakeFiles/razers.dir/param_tabs.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/param_tabs.cpp [ 71%] Linking CXX executable ../../bin/razers cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers.dir/razers.cpp.o CMakeFiles/razers.dir/param_tabs.cpp.o -o ../../bin/razers -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 71%] Built target razers make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 73%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o -MF CMakeFiles/razers3.dir/razers.cpp.o.d -o CMakeFiles/razers3.dir/razers.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:57: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:63: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:34, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:845:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 845 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:862:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 862 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:896:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 896 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:934:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 934 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:968:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 968 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1009:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1009 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1046:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1046 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1087:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1087 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1130:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1130 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1174:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1174 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1218:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1218 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:127:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:83: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:265:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 265 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:321:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 321 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:366:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 366 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:785:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 785 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:97: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1348:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1348:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1348:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1351:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1351 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1351:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1351 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1351:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1351 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1356:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1356:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1356:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1359:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1359:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1359:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1362:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1362 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1362:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1362 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1362:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1362 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:785:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 785 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:785:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 785 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:785:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 785 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:745:69: required from ‘void seqan::write(TTarget&, FragmentStore&, Amos) [with TTarget = VirtualStream >; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 745 | ModifiedString > quals(fragStore.readSeqStore[idCount]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1222:14: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1222 | write(file, store, Amos()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:785:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 785 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:85: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:33: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:68: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment, Alloc<> >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 340 | return TRevComp(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:936:80: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter >, StreamIterator > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 489 | TIter iter = begin(seq, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:740:27: required from ‘void seqan::write(TTarget&, FragmentStore&, Amos) [with TTarget = VirtualStream >; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 740 | writeWrappedString(iter, fragStore.readSeqStore[idCount], 60); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1222:14: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1222 | write(file, store, Amos()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:98:7: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::begin(const ModifiedString&, Tag) [with THost = const Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 98 | class ModifiedIterator > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter >, StreamIterator > >; TSequence = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 489 | TIter iter = begin(seq, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:746:27: required from ‘void seqan::write(TTarget&, FragmentStore&, Amos) [with TTarget = VirtualStream >; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 746 | writeWrappedString(iter, quals, 60); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1222:14: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1222 | write(file, store, Amos()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:223: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1088:24: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1088 | _applyFilterOptions(filterPatternL, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:222: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1088:24: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1088 | _applyFilterOptions(filterPatternL, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1088:24: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1088 | _applyFilterOptions(filterPatternL, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1088:24: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1088 | _applyFilterOptions(filterPatternL, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:969:48: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 969 | pattern.finderLength = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3026 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:2081:73: required from ‘bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2081 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >; TShape = Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 751 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:872:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 872 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 751 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3026 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:872:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 872 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 751 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:969:48: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 969 | pattern.finderLength = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3026 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:2081:73: required from ‘bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2081 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:872:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 872 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3026 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:872:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 872 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >; TShape = Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 751 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 751 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 751 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = String, Alloc<> >; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 466 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:513:15: required from ‘void seqan::insertGap(Gaps&, TPosition) [with TSequence = String, Alloc<> >; TSpec = AnchorGaps, Alloc<> > >; TPosition = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 513 | insertGaps(gaps, clippedViewPos, 1u); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2067:42: required from ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TScore = Score >; TShrinkMatches = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2067 | insertGap(gaps, insPos - rBegin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1221:40: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1221 | convertMatchesToGlobalAlignment(store, scoreType, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:395:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 395 | data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:680:20: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 680 | TFilterFinderR filterFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:932:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 932 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:941:46: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 941 | finder.haystackEnd = begin(host(finder)) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:2088:30: required from ‘bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2088 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:932:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 932 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:2088:30: required from ‘bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2088 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:24: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:529:32: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 529 | _alignAndGetCigarString(cigar, md, contigInfix, readSeq, alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:529:32: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 529 | _alignAndGetCigarString(cigar, md, contigInfix, readSeq, alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:534:32: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 534 | _alignAndGetCigarString(cigar, md, contigInfix, reverseComplementString(readSeq), alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = const Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 663 | TResult tmp(end(host(me), tag_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:811:66: required from ‘void seqan::_fillBamSeqAndQual(TSeq&, TQual&, const TRead&) [with TSeq = String, Alloc<> >; TQual = String >; TRead = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 811 | typename Iterator::Type sIt = begin(read, Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:936:31: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:398:24: required from ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 398 | appendValue(indexText(indexL), readSetL[j]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = const Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:859:24: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 859 | appendValue(indexText(index), store.readSeqStore[j]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:24: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:534:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:654:36: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 654 | TReadSet & readSetL = host(host(filterPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2241:41: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 2241 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2795:64: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2795 | std::cout << " stepsize: " << getStepSize(host(filterPattern)) << std::endl; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1088:24: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:852:30: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 852 | TIndex & index = host(tls.filterPattern); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:852:30: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 852 | TIndex & index = host(tls.filterPattern); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:654:36: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 654 | TReadSet & readSetL = host(host(filterPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:852:30: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 852 | TIndex & index = host(tls.filterPattern); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:989:66: required from ‘bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = const Segment, Alloc<> >, InfixSegment>; TNeedle2 = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 989 | typename Size::Type const columns = length(container(finder)) + state.leftClip; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1181:44: required from ‘bool seqan::_stateInit(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = const Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1181 | return _patternInitSmallStateBanded(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1535:24: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = const Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1535 | if (!_stateInit(finder, needle, state)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1646:16: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = const Segment, Alloc<> >, InfixSegment>; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1646 | return find(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2177:16: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2177 | while (find(myersFinder, readPrefix, state, minScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_interface.h:430:24: required from ‘void seqan::goEnd(TIterator&) [with TIterator = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 430 | goEnd(it, container(it)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:737:10: required from ‘void seqan::goEnd(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 737 | goEnd(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1537:18: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1537 | goEnd(finder); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1646:16: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1646 | return find(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2245:32: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2245 | while (find(myersFinderRev, readRev, verifier.revPatternState, maxScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2948:40: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2948 | TReadSet & readSet = indexText(host(filterPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2795:64: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 2795 | std::cout << " stepsize: " << getStepSize(host(filterPattern)) << std::endl; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3026:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = const Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = const Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2948:40: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2948 | TReadSet & readSet = indexText(host(filterPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 135 | assignValue(*this, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:175:9: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:169:56: required from ‘typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 193 | else return *source(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 275 | return getValue(iter(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_base.h:151:37: required from ‘typename seqan::Convert >::Type seqan::convertImpl(Convert, const Proxy&) [with TTarget = char; T = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; TSpec = IteratorProxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > >; typename Convert >::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 151 | return convert(getValue(source)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_conversion.h:149:23: required from ‘typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; typename Convert::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 149 | return convertImpl(Convert(), source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:241:45: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:46: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:169:56: required from ‘typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 193 | else return *source(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 275 | return getValue(iter(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_alphabet_expansion.h:357:37: required from ‘typename seqan::Convert >, seqan::Proxy >::Type seqan::convertImpl(Convert >, T>, const Proxy&) [with THost = SimpleType; char CHAR = '-'; TSpec = Tag; T = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; TSpec2 = IteratorProxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > >; typename Convert >, Proxy >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 357 | return convert(getValue(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_conversion.h:149:23: required from ‘typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = ModifiedAlphabet, ModExpand<'-'> >; TSource = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; typename Convert::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 149 | return convertImpl(Convert(), source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_alphabet_expansion.h:92:59: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:169:17: required from ‘typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 193 | else return *source(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 275 | return getValue(iter(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_base.h:151:37: required from ‘typename seqan::Convert >::Type seqan::convertImpl(Convert, const Proxy&) [with TTarget = char; T = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; TSpec = IteratorProxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > >; typename Convert >::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 151 | return convert(getValue(source)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_conversion.h:149:23: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:994:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 994 | TConstSeqVIterator itVEnd = begin(seqV, Rooted()) + _min(seqVlength - 1, lowerDiagonal(band) + seqHlength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:612:32: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 612 | _computeHammingDistance(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoringScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 613 | dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:45: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(const ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = ModView > >; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:314:32: required from ‘typename seqan::Position > >::Type seqan::position(const ModifiedIterator >&) [with THost = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 314 | return length(container(host(me))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:675:73: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 675 | sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin)), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:288:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 288 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: required from ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 586 | return Iter >(container(left), hostIterator(left) + right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:169:56: required from ‘typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 193 | else return *source(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 275 | return getValue(iter(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_base.h:151:37: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = ModView > >; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:30: required from ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 278 | TContainer cont(container(host(me))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:397:81: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = SimpleType; TSeqVValue = SimpleType; TSeqVIterator = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >; TScoringScheme = Score >; TDPCell = DPCell_ >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 397 | tmpSeqH, sequenceEntryForScore(scoringScheme, container(iter), position(iter)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:891:38: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 891 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 892 | sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 893 | sequenceEntryForScore(scoringScheme, seqV, 0), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 894 | seqVBegin, seqVEnd, scoringScheme, cacheDiag, cacheVert, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 895 | MetaColumnDescriptor(), dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 889 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 924 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 150 | assign(*this, source_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 519 | class Pattern > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 889 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 924 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 150 | assign(*this, source_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:318:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 318 | class Pattern > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 889 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 924 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 150 | assign(*this, source_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 519 | class Pattern > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 889 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 924 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 150 | assign(*this, source_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:318:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 318 | class Pattern > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 889 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 924 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 150 | assign(*this, source_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 519 | class Pattern > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 889 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 924 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 150 | assign(*this, source_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 519 | class Pattern > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/paramChooser.h:993:51, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/paramChooser.h:1286:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/paramChooser.h:1011:66, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/paramChooser.h:1286:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/paramChooser.h:1021:53, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/paramChooser.h:1286:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 73%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o -MF CMakeFiles/razers3.dir/param_tabs.cpp.o.d -o CMakeFiles/razers3.dir/param_tabs.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/param_tabs.cpp [ 73%] Linking CXX executable ../../bin/razers3 cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3.dir/razers.cpp.o CMakeFiles/razers3.dir/param_tabs.cpp.o -o ../../bin/razers3 -lrt -lz -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 73%] Built target razers3 make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 75%] Building CXX object apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -MF CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o.d -o CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:6: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1035 | return loadContigs(store, fileNames, loadSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:120:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | if (!loadContigs(store, toCString(referenceFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1035 | return loadContigs(store, fileNames, loadSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:120:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | if (!loadContigs(store, toCString(referenceFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1035 | return loadContigs(store, fileNames, loadSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:120:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | if (!loadContigs(store, toCString(referenceFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1035 | return loadContigs(store, fileNames, loadSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:120:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | if (!loadContigs(store, toCString(referenceFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1035 | return loadContigs(store, fileNames, loadSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:120:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | if (!loadContigs(store, toCString(referenceFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 75%] Linking CXX executable ../../bin/razers3_simulate_reads cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_simulate_reads.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -o ../../bin/razers3_simulate_reads -lrt -lz -lbz2 In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 75%] Built target razers3_simulate_reads make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 76%] Building CXX object apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -MF CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o.d -o CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:5: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:6: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:34, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:845:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 845 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:862:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 862 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:896:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 896 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:934:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 934 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:968:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 968 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1009:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1009 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1046:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1046 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1087:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1087 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1130:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1130 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1174:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1174 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1218:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1218 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:42:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:42:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:42:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:42:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:42:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 76%] Linking CXX executable ../../bin/razers3_quality2prob cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_quality2prob.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -o ../../bin/razers3_quality2prob -lrt -lz -lbz2 In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 76%] Built target razers3_quality2prob make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rep_sep /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 78%] Building CXX object apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rep_sep && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.1.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o -MF CMakeFiles/rep_sep.dir/rep_sep.cpp.o.d -o CMakeFiles/rep_sep.dir/rep_sep.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep.cpp:27: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep.cpp:22: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep.cpp:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; TSource = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:702:11: required from ‘void seqan::assignValue(T&, TPos, const TValue&) [with T = String, AlignedReadStoreElement, void>, long unsigned int>, Alloc<> >; TValue = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; TPos = unsigned int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 702 | assign(value(me, pos), _value); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/property_map_generic.h:186:16: required from ‘typename seqan::EnableIf >, void>::Type seqan::assignProperty(TPropertyMap&, TDescriptor, TValue) [with TPropertyMap = String, AlignedReadStoreElement, void>, long unsigned int>, Alloc<> >; TDescriptor = unsigned int; TValue = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; typename EnableIf >, void>::Type = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 186 | assignValue(pm, _getId(d), val); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rgraph_base.h:191:23: required from ‘GraphCargo& registerRead(ReadGraph&, typename ReadGraph::TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int; typename ReadGraph::TId = unsigned int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 191 | assignProperty(me.vertexCargo, vd, new_cargo); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rgraph_construction.h:82:59: required from ‘void construct(ReadGraph&, const seqan::String > >&, const seqan::FragmentStore&, TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int; TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 82 | TGraphCargo & new_cargo = registerRead(me, _readId(value(colIter))); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep.cpp:217:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 217 | construct(rgraph, candidates, fragStore, options.contig); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>& GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>::operator=(const GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rgraph.h:32, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep.cpp:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rgraph_base.h:44:5: note: because ‘GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>’ has user-provided ‘GraphCargo::GraphCargo(const GraphCargo&) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int]’ 44 | GraphCargo(GraphCargo const& other) | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast >, seqan::PrefixSegment> >(seqan::Segment >, seqan::PrefixSegment> const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast >, seqan::PrefixSegment> >(unsigned int const&, seqan::Segment >, seqan::PrefixSegment> const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast >, seqan::SuffixSegment> >(seqan::Segment >, seqan::SuffixSegment> const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast >, seqan::SuffixSegment> >(unsigned int const&, seqan::Segment >, seqan::SuffixSegment> const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast >, seqan::PrefixSegment> >(seqan::Segment >, seqan::PrefixSegment> const&)long’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const long int &’ to ‘seqan::BadLexicalCast::BadLexicalCast >, seqan::PrefixSegment> >(long const&, seqan::Segment >, seqan::PrefixSegment> const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast >, seqan::SuffixSegment> >(seqan::Segment >, seqan::SuffixSegment> const&)long’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const long int &’ to ‘seqan::BadLexicalCast::BadLexicalCast >, seqan::SuffixSegment> >(long const&, seqan::Segment >, seqan::SuffixSegment> const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)long’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const long int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(long const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 78%] Linking CXX executable ../../bin/rep_sep cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rep_sep && /usr/bin/cmake -E cmake_link_script CMakeFiles/rep_sep.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rep_sep.dir/rep_sep.cpp.o -o ../../bin/rep_sep -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_undirected.h:357:36, inlined from ‘registerRead’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rgraph_base.h:187:41, inlined from ‘construct’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rgraph_construction.h:82:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘construct’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 78%] Built target rep_sep make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 78%] Building CXX object apps/sak/CMakeFiles/sak.dir/sak.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/sak/CMakeFiles/sak.dir/sak.cpp.o -MF CMakeFiles/sak.dir/sak.cpp.o.d -o CMakeFiles/sak.dir/sak.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:337:23: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 337 | openRes = open(inFile, toCString(options.inFastxPath)); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:337:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 337 | openRes = open(inFile, toCString(options.inFastxPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:337:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 337 | openRes = open(inFile, toCString(options.inFastxPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:337:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 337 | openRes = open(inFile, toCString(options.inFastxPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:347:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | openRes = open(outFile, toCString(options.outPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:337:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 337 | openRes = open(inFile, toCString(options.inFastxPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:347:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | openRes = open(outFile, toCString(options.outPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 489 | TIter iter = begin(seq, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:468:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 468 | writeWrappedString(target, seq, lineLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 506 | writeRecord(file, meta, seq, qual, TFormat()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 519 | writeRecord(file, meta, seq, qual, file.format); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:424:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment >, InfixSegment>; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 489 | TIter iter = begin(seq, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:475:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 475 | writeWrappedString(target, qual, lineLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 506 | writeRecord(file, meta, seq, qual, TFormat()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 519 | writeRecord(file, meta, seq, qual, file.format); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:424:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 489 | TIter iter = begin(seq, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:468:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 468 | writeWrappedString(target, seq, lineLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 506 | writeRecord(file, meta, seq, qual, TFormat()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 519 | writeRecord(file, meta, seq, qual, file.format); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:424:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment >, InfixSegment>; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 489 | TIter iter = begin(seq, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:475:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 475 | writeWrappedString(target, qual, lineLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 506 | writeRecord(file, meta, seq, qual, TFormat()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 519 | writeRecord(file, meta, seq, qual, file.format); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:424:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 79%] Linking CXX executable ../../bin/sak cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak && /usr/bin/cmake -E cmake_link_script CMakeFiles/sak.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sak.dir/sak.cpp.o -o ../../bin/sak -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 79%] Built target sak make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sam2matrix /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 79%] Building CXX object apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sam2matrix && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -MF CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o.d -o CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 257 | _open(*this, fileName, openMode, True()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:173:59: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 173 | BamFileIn bamIO(toCString(options.samFileNames[i])); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:173:59: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 173 | BamFileIn bamIO(toCString(options.samFileNames[i])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘_parseSamFiles(seqan::StringSet >, seqan::Owner > >&, std::map >, unsigned int, std::less > >, std::allocator > const, unsigned int> > >&, SamToGasicOptions const&)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:181:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘_parseSamFiles(seqan::StringSet >, seqan::Owner > >&, std::map >, unsigned int, std::less > >, std::allocator > const, unsigned int> > >&, SamToGasicOptions const&)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘_parseSamFiles(seqan::StringSet >, seqan::Owner > >&, std::map >, unsigned int, std::less > >, std::allocator > const, unsigned int> > >&, SamToGasicOptions const&)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:181:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘_parseSamFiles(seqan::StringSet >, seqan::Owner > >&, std::map >, unsigned int, std::less > >, std::allocator > const, unsigned int> > >&, SamToGasicOptions const&)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘_parseSamFiles(seqan::StringSet >, seqan::Owner > >&, std::map >, unsigned int, std::less > >, std::allocator > const, unsigned int> > >&, SamToGasicOptions const&)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:181:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘_parseSamFiles(seqan::StringSet >, seqan::Owner > >&, std::map >, unsigned int, std::less > >, std::allocator > const, unsigned int> > >&, SamToGasicOptions const&)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 81%] Linking CXX executable ../../bin/sam2matrix cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sam2matrix && /usr/bin/cmake -E cmake_link_script CMakeFiles/sam2matrix.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -o ../../bin/sam2matrix -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 81%] Built target sam2matrix make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/samcat /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 81%] Building CXX object apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/samcat && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o -MF CMakeFiles/samcat.dir/samcat.cpp.o.d -o CMakeFiles/samcat.dir/samcat.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat/samcat.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat/samcat.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat/samcat.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat/samcat.cpp:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord >, seqan::AdaptorIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter >, seqan::AdaptorIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord >, seqan::AdaptorIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter >, seqan::AdaptorIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 81%] Linking CXX executable ../../bin/samcat cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/samcat && /usr/bin/cmake -E cmake_link_script CMakeFiles/samcat.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/samcat.dir/samcat.cpp.o -o ../../bin/samcat -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 81%] Built target samcat make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 81%] Building CXX object apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin && /usr/bin/g++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o -MF CMakeFiles/s4_search.dir/search.cpp.o.d -o CMakeFiles/s4_search.dir/search.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/parallel/base.h:36, from /usr/include/c++/14/parallel/algobase.h:40, from /usr/include/c++/14/parallel/algorithm:36, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:282:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 282 | index(searcher); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:142: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:323:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 323 | prepare(searcher, query); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:282:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 282 | index(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:323:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 323 | prepare(searcher, query); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:405:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 405 | index(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:449:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 449 | prepare(searcher, queryLong); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:405:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 405 | index(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:449:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 449 | prepare(searcher, queryLong); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:138: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:57: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 810 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:508:31: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 508 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter > >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 810 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:536:31: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 536 | return runSearcher(options, TDbGeo(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, Tag, Writer > >, Owner > >, void>, Db > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, Tag, Writer > >, Owner > >, void>, Db > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, Tag, Writer > >, Owner > >, void>, Db > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, Tag, Writer > >, Owner > >, void>, Db > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc > >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 810 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:508:31: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 508 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment > >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter > >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 810 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:536:31: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 536 | return runSearcher(options, TDbGeo(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:132:10: required from ‘void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 132 | write(writer.outputIt, id1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:150:17: required from ‘void _write(Writer&, typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 150 | _writeRecord(writer, writer.db.ids[dbId], writer.query.ids[queryId]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:98:15: required from ‘void Writer::operator()(typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 98 | _write(*this, dbId, queryId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:142:13: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 142 | delegate(dbId, queryId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 810 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:508:31: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 508 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:132:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:98:15: required from ‘void Writer::operator()(typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 98 | _write(*this, dbId, queryId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:142:13: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 142 | delegate(dbId, queryId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 810 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:508:31: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 508 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 302 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:320:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ [ 82%] Linking CXX executable ../../bin/s4_search cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin && /usr/bin/cmake -E cmake_link_script CMakeFiles/s4_search.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/s4_search.dir/search.cpp.o -o ../../bin/s4_search -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:280:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:290:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘operator++.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:345:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign.constprop.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘assign.constprop.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 82%] Built target s4_search make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 82%] Building CXX object apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin && /usr/bin/g++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o -MF CMakeFiles/s4_join.dir/join.cpp.o.d -o CMakeFiles/s4_join.dir/join.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/parallel/base.h:36, from /usr/include/c++/14/parallel/algobase.h:40, from /usr/include/c++/14/parallel/algorithm:36, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:355:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 264 | index(joiner); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:319:37: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 319 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Exact()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:142: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:279:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 279 | prepare(joiner, db); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:355:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:332:37: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Exact()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:279:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 279 | prepare(joiner, db); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:355:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:357:37: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 357 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Exact()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:279:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 279 | prepare(joiner, db); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:355:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:370:37: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 370 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Exact()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:279:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 279 | prepare(joiner, db); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:138: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:57: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:311:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:132:10: required from ‘void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 132 | write(writer.outputIt, id1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:197:21: required from ‘bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 197 | _writeRecord(writer, writer.db.ids[dbId], writer.db.ids[dbId]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:293:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 293 | close(writer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:311:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter > >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:349:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 349 | return runJoiner(options, TDbGeo(), Nothing(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc > >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:311:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:132:10: required from ‘void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 132 | write(writer.outputIt, id1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:197:21: required from ‘bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 197 | _writeRecord(writer, writer.db.ids[dbId], writer.db.ids[dbId]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:293:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 293 | close(writer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:311:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment > >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter > >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:349:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 349 | return runJoiner(options, TDbGeo(), Nothing(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 302 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:320:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ [ 84%] Linking CXX executable ../../bin/s4_join cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin && /usr/bin/cmake -E cmake_link_script CMakeFiles/s4_join.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/s4_join.dir/join.cpp.o -o ../../bin/s4_join -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘operator++.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:345:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:280:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:290:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign.constprop.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘assign.constprop.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 84%] Built target s4_join make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqan_tcoffee /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 85%] Building CXX object apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqan_tcoffee && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.13.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -MF CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o.d -o CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:37, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:22: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervalsExcludeTouching(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String > > > >; TValue = long unsigned int; TCargo = Pair >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from ‘void seqan::matchRefinement(TAlignmentString&, StringSet&, TScore&, TOutGraph&, typename Size::Type>::Type, TAnnotation&, Tag) [with TAlignmentString = String >; TAnnotation = bool; TOutGraph = Graph, Alloc<> >, Dependent > >, long unsigned int, Tag > >; TSequence = String, Alloc<> >; TSetSpec = Dependent >; TScore = long unsigned int; TTagSpec = TagExactRefinement_; typename Size::Type>::Type = long unsigned int; typename Value::Type = Fragment<>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 571 | findIntervalsExcludeTouching(relevant_segments, gs[seq_i_pos],pms[seq_i_pos],node_i); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from ‘void seqan::matchRefinement(TFragmentString&, StringSet&, TOutGraph&) [with TFragmentString = String >; TOutGraph = Graph, Alloc<> >, Dependent > >, long unsigned int, Tag > >; TSequence = String, Alloc<> >; TSetSpec = Dependent >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 678 | matchRefinement(matches,strSet,fake_score,ali_graph,1,anno,ExactRefinement()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:191:20: required from ‘void seqan::buildAlignmentGraph(String&, Graph >&, FrequencyCounting) [with TFragment = Fragment<>; TSpec1 = Alloc<>; TStringSet = StringSet, Alloc<> >, Dependent > >; TCargo = long unsigned int; TSpec = Tag; FrequencyCounting = const Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 191 | matchRefinement(matches,strSet,outGraph); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_msa.h:178:24: required from ‘void seqan::evaluateAlignment(const MsaOptions&) [with TAlphabet = SimpleType; TScore = Score, Tag > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 178 | buildAlignmentGraph(matches, g, FrequencyCounting()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:281:26: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 281 | evaluateAlignment(msaOpt); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 305 | _initMsaParams(parser, sc); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1667 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1679 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1701 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned long’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const long unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned long const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read >, seqan::Fragment > >, seqan::Alloc, int, seqan::Alloc, seqan::StringSet >, seqan::Owner > > >(std::basic_ifstream >&, seqan::String > >, seqan::Alloc >&, seqan::String >&, seqan::StringSet >, seqan::Owner > > const&, seqan::Tag)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_io.h:209:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::read >, seqan::Fragment > >, seqan::Alloc, int, seqan::Alloc, seqan::StringSet >, seqan::Owner > > >(std::basic_ifstream >&, seqan::String > >, seqan::Alloc >&, seqan::String >&, seqan::StringSet >, seqan::Owner > > const&, seqan::Tag)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 85%] Linking CXX executable ../../bin/seqan_tcoffee cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqan_tcoffee && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqan_tcoffee.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -o ../../bin/seqan_tcoffee -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 85%] Built target seqan_tcoffee make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 87%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons.cpp.o -MF CMakeFiles/seqcons2.dir/seqcons.cpp.o.d -o CMakeFiles/seqcons2.dir/seqcons.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 87%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_app.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_app.cpp.o -MF CMakeFiles/seqcons2.dir/seqcons_app.cpp.o.d -o CMakeFiles/seqcons2.dir/seqcons_app.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/unique_ptr.h:38, from /usr/include/c++/14/memory:78, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:88:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 88 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:99:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1618:57: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1618 | TContigIterator cit = begin(contigGaps, Standard()) + (_min(alignedRead.beginPos, alignedRead.endPos) + beginPosition(readGaps)); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:145:27: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 145 | printAlignment(out, layout, store, /*contigID=*/contigID, /*beginPos=*/0, /*endPos=*/endPos, 0, 100); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:116:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 116 | if (!open(seqFileOut, options.outputFileConsensus.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:32: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:145:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 145 | printAlignment(out, layout, store, /*contigID=*/contigID, /*beginPos=*/0, /*endPos=*/endPos, 0, 100); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:87, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:55: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:145:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 145 | printAlignment(out, layout, store, /*contigID=*/contigID, /*beginPos=*/0, /*endPos=*/endPos, 0, 100); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h: In instantiation of ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, TProfileString&, seqan::ExtractProfileInfo_&, TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1138 | _subtractReadAlignment(windowBegin, windowEnd, profilePart, info, *it, it - begin(contigAlignedReads, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:404:32: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 404 | for (TReadGapsIter itR2 = itR; itR2 != itREnd; ++itR2) | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:116:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 116 | if (!open(seqFileOut, options.outputFileConsensus.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:32: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:145:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 145 | printAlignment(out, layout, store, /*contigID=*/contigID, /*beginPos=*/0, /*endPos=*/endPos, 0, 100); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:55: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:145:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 145 | printAlignment(out, layout, store, /*contigID=*/contigID, /*beginPos=*/0, /*endPos=*/endPos, 0, 100); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:116:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 116 | if (!open(seqFileOut, options.outputFileConsensus.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment, Alloc<> >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 340 | return TRevComp(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:936:80: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1109 | writeAlignments(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1118 | writeRecords(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:153:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 153 | writeRecords(out, store); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:223:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 223 | if (!open(seqFileIn, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:223: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:370:17: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 370 | _patternInit(filterPattern, maxErrorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = unsigned int; TTag = Standard_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:395:33: required from ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, TProfileString&, seqan::ExtractProfileInfo_&, TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 395 | TReadGapsIter itR = iter(readGaps, windowInfo.readAliBeginPos, Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1138 | _subtractReadAlignment(windowBegin, windowEnd, profilePart, info, *it, it - begin(contigAlignedReads, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:408:48: required from ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, TProfileString&, seqan::ExtractProfileInfo_&, TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 408 | std::cerr << convert(*itR2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1138 | _subtractReadAlignment(windowBegin, windowEnd, profilePart, info, *it, it - begin(contigAlignedReads, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:98:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 98 | class ModifiedIterator > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:811:66: required from ‘void seqan::_fillBamSeqAndQual(TSeq&, TQual&, const TRead&) [with TSeq = String, Alloc<> >; TQual = String >; TRead = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 811 | typename Iterator::Type sIt = begin(read, Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:936:31: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1109 | writeAlignments(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1118 | writeRecords(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:153:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 153 | writeRecords(out, store); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:223:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 223 | if (!open(seqFileIn, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = const Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole<>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:969:48: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = const Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 969 | pattern.finderLength = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:377:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | while (find(filterFinder, filterPattern, maxErrorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:376:20: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 376 | appendValue(seqs, store.readSeqStore[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 369 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:279:37: required from ‘void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(TProfileString&, TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 279 | for (TReadSeqIter it = begin(store.readSeqStore[el.readId]), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1020:13: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1020 | _getReadAsProfile(contigProfile, contigAlignedReads[0]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:504:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 504 | return end(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:280:33: required from ‘void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(TProfileString&, TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 280 | itEnd = end(store.readSeqStore[el.readId]); it != itEnd; ++it, ++itP) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1020:13: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1020 | _getReadAsProfile(contigProfile, contigAlignedReads[0]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:408:48: required from ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, TProfileString&, seqan::ExtractProfileInfo_&, TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 408 | std::cerr << convert(*itR2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1138 | _subtractReadAlignment(windowBegin, windowEnd, profilePart, info, *it, it - begin(contigAlignedReads, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = unsigned int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = unsigned int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = String, Alloc<> >; TGapAnchors = String, Alloc<> >; TPosition = unsigned int; TCount = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 466 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:930:19: required from ‘void seqan::AnsonMyersRealigner_::_endContig(unsigned int) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 930 | insertGaps(contigGaps, gaps[i].i1, gaps[i].i2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:697:5: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 697 | _endContig(contigID); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:572:29: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, BamAlignFunctorDefault&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 572 | errors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1109 | writeAlignments(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1118 | writeRecords(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:153:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 153 | writeRecords(out, store); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 140 | _host(std::forward(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment, Alloc<> >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 340 | return TRevComp(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:936:80: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1109 | writeAlignments(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1118 | writeRecords(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:153:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 153 | writeRecords(out, store); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:229:32: required from ‘seqan::Finder >::Finder(THaystack&) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 229 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:376:23: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 376 | TFilterFinder filterFinder(*it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = const Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole<>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:932:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole<> >; TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 932 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = const Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:377:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | while (find(filterFinder, filterPattern, maxErrorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:941:46: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole<> >; TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 941 | finder.haystackEnd = begin(host(finder)) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = const Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:377:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | while (find(filterFinder, filterPattern, maxErrorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervalsExcludeTouching(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String > > > >; TValue = long unsigned int; TCargo = Pair >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from ‘void seqan::matchRefinement(TAlignmentString&, StringSet&, TScore&, TOutGraph&, typename Size::Type>::Type, TAnnotation&, Tag) [with TAlignmentString = String >; TAnnotation = bool; TOutGraph = Graph, Alloc<> >, InfixSegment>, Dependent > >, unsigned int, Tag > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSetSpec = Dependent >; TScore = unsigned int; TTagSpec = TagExactRefinement_; typename Size::Type>::Type = long unsigned int; typename Value::Type = Fragment<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 571 | findIntervalsExcludeTouching(relevant_segments, gs[seq_i_pos],pms[seq_i_pos],node_i); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from ‘void seqan::matchRefinement(TFragmentString&, StringSet&, TOutGraph&) [with TFragmentString = String >; TOutGraph = Graph, Alloc<> >, InfixSegment>, Dependent > >, unsigned int, Tag > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSetSpec = Dependent >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 678 | matchRefinement(matches,strSet,fake_score,ali_graph,1,anno,ExactRefinement()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:136:20: required from ‘void seqan::buildAlignmentGraph(String&, String&, Graph >&, FractionalScore) [with TFragment = Fragment<>; TSpec1 = Alloc<>; TScoreValue = int; TSpec2 = Alloc<>; TStringSet = StringSet, Alloc<> >, InfixSegment>, Dependent > >; TCargo = unsigned int; TSpec = Tag; FractionalScore = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 136 | matchRefinement(matches,strSet,outGraph); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:272:24: required from ‘void seqan::buildAlignmentGraph(String&, String&, Graph >&, const TScore&, ReScore) [with TFragment = Fragment<>; TSpec1 = Alloc<>; TScoreValue = int; TSpec2 = Alloc<>; TStringSet = StringSet, Alloc<> >, InfixSegment>, Dependent > >; TCargo = unsigned int; TSpec = Tag; TScore = Score >; ReScore = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 272 | buildAlignmentGraph(matches, scores, outGraph, FractionalScore() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:384:24: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 384 | buildAlignmentGraph(fragments, scores, inGraph, msaScoringScheme, ReScore()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1667 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1679 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1701 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = String, Alloc<> >; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 466 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:295:23: required from ‘bool seqan::alignmentGraphToFragmentStore(TFragmentStore&, const Graph, TCargo, TSpec> >&, const Graph >&, const String >&, const String >&, unsigned int, bool) [with TFragmentStore = FragmentStore<>; TSequence = Segment, Alloc<> >, InfixSegment>; TCargo = unsigned int; TSetSpec = Dependent >; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 295 | insertGaps(gaps, from - store.alignedReadStore[*itS].beginPos, fLen); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:427:34: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 427 | alignmentGraphToFragmentStore(store, graph, distances, component, order, numComponents, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 428 | /*logging=*/(options.verbosity >= 3)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:572:29: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, BamAlignFunctorDefault&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 572 | errors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1109 | writeAlignments(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1118 | writeRecords(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:153:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 153 | writeRecords(out, store); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:352:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 352 | appendValue(superSet, store.readSeqStore[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:376:20: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 376 | appendValue(seqs, store.readSeqStore[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:376:20: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 376 | appendValue(seqs, store.readSeqStore[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:162:56: required from ‘typename seqan::Source > > >::Type seqan::source(Iter > >&) [with TGaps = const Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 162 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:183:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(Iter > >&) [with TGaps = const Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 183 | else return *source(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:950:54: required from ‘void seqan::write(TTarget&, const Gaps&) [with TTarget = Iter, StreamIterator > >; TSource = Segment, Alloc<> >, InfixSegment>; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 950 | writeValue(target, convert(getValue(begin_))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:965:10: required from ‘TTarget& seqan::operator<<(TTarget&, const Gaps&) [with TTarget = std::basic_ostream; TSource = Segment, Alloc<> >, InfixSegment>; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 965 | write(it, gaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:363:40: required from ‘void seqan::AnsonMyersRealignmentRound_::_computeReadClippingInfo(seqan::WindowClippingInfo_&, const TAlignedReadElement&, unsigned int, unsigned int) [with TFragmentStore = seqan::FragmentStore<>; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 363 | std::cerr << "READ GAPS\t" << readGaps << "\n"; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1067:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1067 | _computeReadClippingInfo(windowInfo, *it, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = int; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = Segment, Alloc<> >, InfixSegment>; TGapAnchors = String, Alloc<> >; TPosition = int; TCount = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 466 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:513:15: required from ‘void seqan::insertGap(Gaps&, TPosition) [with TSequence = Segment, Alloc<> >, InfixSegment>; TSpec = AnchorGaps, Alloc<> > >; TPosition = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 513 | insertGaps(gaps, clippedViewPos, 1u); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1610:30: required from ‘void seqan::AnsonMyersRealignmentRound_::_updateAlignments(unsigned int, unsigned int&, TProfileString&, seqan::Gaps::Type>::Type>::Type> > >&, seqan::Gaps::Type>&, seqan::ExtractProfileInfo_&, const seqan::WindowClippingInfo_&, const TAlignedReadIter&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; typename seqan::BaseAlphabet::Type>::Type>::Type = seqan::SimpleType; typename seqan::Value::Type>::Type = seqan::SimpleType; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename TFragmentStore::TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1610 | insertGap(anchorReadGaps, readGapsPos++); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1321:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1321 | _updateAlignments(windowBegin, windowEnd, profilePart, profileGaps, readGaps, info, windowInfo, it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = Segment, Alloc<> >, InfixSegment>; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 466 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2236:27: required from ‘void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = AlignedReadStoreElement, void>*; TPos = long int; TSize = long int; TReadSeqStore = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 2236 | insertGaps(gaps, insPos - rBegin, blkLen); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2321:40: required from ‘void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = Gaps, AnchorGaps, Alloc<> > > >; TContigGapsPW = Gaps, AnchorGaps, Alloc<> >, InfixSegment> > >; TReadGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TAlignedReadIter = AlignedReadStoreElement, void>*; TReadSeqStore = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 2321 | _alignedReadsInsertGaps(overlappingAlignedReadsBegin1, overlappingAlignedReadsEnd1, insPos, blkLen, readSeqStore); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2437:31: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 2437 | _twoWayMergeAlignments( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~^ 2438 | contigGapsGlobal, contigGapsPW, readGaps, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2439 | firstOverlapOld, lastOverlapOld, firstOverlapNew, it, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2440 | store.readSeqStore); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:337:41: required from ‘void seqan::readRecords(FragmentStore&, BamIOContext&, TForwardIter&, const TFormat&, const FragStoreImportFlags&) [with TSpec = void; TConfig = FragmentStoreConfig; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >; TForwardIter = Iter >, StreamIterator > >; TFormat = TagSelector, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 337 | convertPairWiseToGlobalAlignment(store, contigAnchorGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&, const FragStoreImportFlags&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 373 | readRecords(store, bamFile, FragStoreImportFlags()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:261:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 261 | readRecords(store, bamFileIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:229:32: required from ‘seqan::Finder >::Finder(THaystack&) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 229 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:376:23: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 376 | TFilterFinder filterFinder(*it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:162:17: required from ‘typename seqan::Source > > >::Type seqan::source(Iter > >&) [with TGaps = const Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 162 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:183:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(Iter > >&) [with TGaps = const Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 183 | else return *source(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:950:54: required from ‘void seqan::write(TTarget&, const Gaps&) [with TTarget = Iter, StreamIterator > >; TSource = Segment, Alloc<> >, InfixSegment>; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 950 | writeValue(target, convert(getValue(begin_))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:965:10: required from ‘TTarget& seqan::operator<<(TTarget&, const Gaps&) [with TTarget = std::basic_ostream; TSource = Segment, Alloc<> >, InfixSegment>; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 965 | write(it, gaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:363:40: required from ‘void seqan::AnsonMyersRealignmentRound_::_computeReadClippingInfo(seqan::WindowClippingInfo_&, const TAlignedReadElement&, unsigned int, unsigned int) [with TFragmentStore = seqan::FragmentStore<>; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 363 | std::cerr << "READ GAPS\t" << readGaps << "\n"; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1067:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1067 | _computeReadClippingInfo(windowInfo, *it, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 135 | assignValue(*this, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:165:9: required from ‘seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 165 | data_gaps(anchors), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2393:29: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2393 | TContigGapsPW contigGapsPW(/*contigInfix, */gaps[it->id - offsetRecord]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:337:41: required from ‘void seqan::readRecords(FragmentStore&, BamIOContext&, TForwardIter&, const TFormat&, const FragStoreImportFlags&) [with TSpec = void; TConfig = FragmentStoreConfig; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >; TForwardIter = Iter >, StreamIterator > >; TFormat = TagSelector, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 337 | convertPairWiseToGlobalAlignment(store, contigAnchorGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&, const FragStoreImportFlags&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 373 | readRecords(store, bamFile, FragStoreImportFlags()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:261:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 261 | readRecords(store, bamFileIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:352:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 352 | appendValue(superSet, store.readSeqStore[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:352:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 352 | appendValue(superSet, store.readSeqStore[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole<>; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:463:41: required from ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 463 | TSize seqCount = countSequences(host(pattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:370:17: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 370 | _patternInit(filterPattern, maxErrorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = const seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: required from ‘TScoreValue seqan::globalAlignment(Align&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequence = Segment, Alloc<> >, InfixSegment>; TAlignSpec = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = true; bool RIGHT = true; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 99 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 | scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 354 | globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag, Gotoh()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; TFragments = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 138 | if (overlapper.computeOverlap(ovl, frags, store.readSeqStore[it->seq0], store.readSeqStore[it->seq1], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | OverlapCandidate_(it->seq0, it->seq1, it->pos1 - it->numErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 | it->pos1 + it->numErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 370 | computeOverlaps(fragments, scores, distances, store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: required from ‘TScoreValue seqan::globalAlignment(Align&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequence = Segment, Alloc<> >, InfixSegment>; TAlignSpec = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = true; bool RIGHT = true; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 99 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 | scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 354 | globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag, Gotoh()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; TFragments = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 138 | if (overlapper.computeOverlap(ovl, frags, store.readSeqStore[it->seq0], store.readSeqStore[it->seq1], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | OverlapCandidate_(it->seq0, it->seq1, it->pos1 - it->numErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 | it->pos1 + it->numErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 370 | computeOverlaps(fragments, scores, distances, store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: required from ‘TScoreValue seqan::globalAlignment(Align&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequence = Segment, Alloc<> >, InfixSegment>; TAlignSpec = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = true; bool RIGHT = true; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 99 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 | scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 354 | globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag, Gotoh()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; TFragments = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 138 | if (overlapper.computeOverlap(ovl, frags, store.readSeqStore[it->seq0], store.readSeqStore[it->seq1], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | OverlapCandidate_(it->seq0, it->seq1, it->pos1 - it->numErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 | it->pos1 + it->numErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 370 | computeOverlaps(fragments, scores, distances, store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: required from ‘TScoreValue seqan::globalAlignment(Align&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequence = Segment, Alloc<> >, InfixSegment>; TAlignSpec = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = true; bool RIGHT = true; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 99 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 | scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 354 | globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag, Gotoh()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; TFragments = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 138 | if (overlapper.computeOverlap(ovl, frags, store.readSeqStore[it->seq0], store.readSeqStore[it->seq1], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | OverlapCandidate_(it->seq0, it->seq1, it->pos1 - it->numErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 | it->pos1 + it->numErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 370 | computeOverlaps(fragments, scores, distances, store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 354 | globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag, Gotoh()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; TFragments = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 138 | if (overlapper.computeOverlap(ovl, frags, store.readSeqStore[it->seq0], store.readSeqStore[it->seq1], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | OverlapCandidate_(it->seq0, it->seq1, it->pos1 - it->numErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 | it->pos1 + it->numErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 370 | computeOverlaps(fragments, scores, distances, store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:382:27: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = ConsensusScoreSequenceEntry >, Alloc<> > >; TSeqVValue = ConsensusScoreSequenceEntry, Alloc<> >, InfixSegment> >; TSeqVIterator = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TScoringScheme = Score >, Score > > >; TDPCell = DPCell_ >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 382 | for (; iter != seqEnd - 1; ++iter) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:453:18: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = ConsensusScoreSequenceEntry >, Alloc<> > >; TSeqVValue = ConsensusScoreSequenceEntry, Alloc<> >, InfixSegment> >; TSeqVIterator = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TScoringScheme = Score >, Score > > >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 453 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqHValue, seqVValue, seqBegin, seqEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 454 | scoringScheme, cacheDiag, cacheVert, TColumnDescriptor{}, TDPProfile{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:515:18: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWise&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = String >, Alloc<> >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >, Score > > >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWise = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 515 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 516 | sequenceEntryForScore(scoringScheme, seqH, 0), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 517 | sequenceEntryForScore(scoringScheme, seqV, 0), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 518 | seqVBegin, seqVEnd, scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 519 | MetaColumnDescriptor(), dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = String >, Alloc<> >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >, Score > > >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = String >, Alloc<> >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = WeightedConsensusScore >, Score > >; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:639:20: required from ‘void seqan::_readToProfileAlignment(TProfileGaps&, TReadGaps&, const TConsensusScore&, const TAlignConfig&, int&, int&, const TAlgoTag&) [with TProfileGaps = Gaps >, Alloc<> >, Tag >; TReadGaps = Gaps, Alloc<> >, InfixSegment>, Tag >; TConsensusScore = Score >, Score > > >; TAlignConfig = AlignConfig; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 639 | globalAlignment(profileGaps, readGaps, consScore, alignConfig, /*lowerBand, upperBand, */tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:657:36: required from ‘void seqan::_readToProfileAlignment(TProfileGaps&, TReadGaps&, const TConsensusScore&, const TAlignConfig&, int&, int&, bool) [with TProfileGaps = Gaps >, Alloc<> >, Tag >; TReadGaps = Gaps, Alloc<> >, InfixSegment>, Tag >; TConsensusScore = Score >, Score > > >; TAlignConfig = AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 657 | _readToProfileAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 658 | NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1209:36: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1209 | _readToProfileAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand, linear); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::TagSelector, seqan::TagList, void> > > >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:573:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::TagSelector, seqan::TagList, void> > > >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::TagSelector, seqan::TagList, void> > > >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:573:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::TagSelector, seqan::TagList, void> > > >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::TagSelector, seqan::TagList, void> > > >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:573:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::TagSelector, seqan::TagList, void> > > >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 89%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_options.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -MF CMakeFiles/seqcons2.dir/seqcons_options.cpp.o.d -o CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_options.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_options.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_options.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_options.h:39: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 89%] Linking CXX executable ../../bin/seqcons2 cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqcons2.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/seqcons2.dir/seqcons.cpp.o CMakeFiles/seqcons2.dir/seqcons_app.cpp.o CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -o ../../bin/seqcons2 -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_undirected.h:357:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_undirected.h:164:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1136:19, inlined from ‘upgmaTree’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:803:12, inlined from ‘upgmaTree’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:892:14, inlined from ‘run’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:397:14: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551600’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘run’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 89%] Built target seqcons2 make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sgip /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 90%] Building CXX object apps/sgip/CMakeFiles/sgip.dir/sgip.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sgip && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/sgip/CMakeFiles/sgip.dir/sgip.cpp.o -MF CMakeFiles/sgip.dir/sgip.cpp.o.d -o CMakeFiles/sgip.dir/sgip.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.cpp:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.cpp:27: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip_base.h:33, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.cpp:33: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 90%] Linking CXX executable ../../bin/sgip cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sgip && /usr/bin/cmake -E cmake_link_script CMakeFiles/sgip.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sgip.dir/sgip.cpp.o -o ../../bin/sgip -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_undirected.h:357:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘addEdges’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:735:43, inlined from ‘_createUndir’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip_base.h:358:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_createUndir’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_undirected.h:357:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘addEdges’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:736:29, inlined from ‘_createUndir’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip_base.h:358:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_createUndir’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘addEdges’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:735:43, inlined from ‘_createGraph.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.h:99:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_createGraph.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘addEdges’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:736:29, inlined from ‘_createGraph.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.h:99:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_createGraph.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addEdge’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:604:22, inlined from ‘addEdges’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:740:16, inlined from ‘_createGraph.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.h:99:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_createGraph.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 90%] Built target sgip make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/snp_store /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 92%] Building CXX object apps/snp_store/CMakeFiles/snp_store.dir/snp_store.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/snp_store && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/snp_store/CMakeFiles/snp_store.dir/snp_store.cpp.o -MF CMakeFiles/snp_store.dir/snp_store.cpp.o.d -o CMakeFiles/snp_store.dir/snp_store.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:31: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:33: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:88:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 88 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:99:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:53: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:356:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 356 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:405:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 405 | struct LessPosLen : public ::std::binary_function < TPosLen, TPosLen, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:420:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 420 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:468:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 468 | struct LessId : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:481:37: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 481 | struct LessGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:504:40: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 504 | struct LessGPosEnd : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:523:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 523 | struct LessGPosEndOa : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:545:36: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 545 | struct HigherQ : public ::std::binary_function < TQual, TQual, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:54, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/pair_base.h: In instantiation of ‘seqan::Pair::Pair(const T1&, const T2&) [with T1 = unsigned int; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:5148:46: required from ‘void seqan::dumpShortIndelPolymorphismsBatch(TFragmentStore&, TReadCigars&, TGenome&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCigars = StringSet > >; TGenome = String, Alloc<> >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 5148 | Pair(1,rInf))); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:971:74: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 971 | if(!options.realign) dumpShortIndelPolymorphismsBatch(fragmentStore, readCigars, fragmentStore.contigStore[0].seq, genomeNames[i], startCoord, currentWindowBegin, currentWindowEnd, indelFileStream, options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 1412 | int result = detectSNPs(options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/pair_base.h:120:53: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 120 | Pair(T1 const & _i1, T2 const & _i2) : i1(_i1), i2(_i2) {} | ^~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 77 | if (!open(seqFileIn, toCString(fileNameList[filecount]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 670 | if(result == CALLSNPS_GENOME_FAILED || !loadGenomes(genomes, genomeFileNameList, gIdStringToIdNumMap, genomeNames)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:4057:36: required from ‘void seqan::dumpVariantsRealignBatch(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCounts = String >; TReadCigars = StringSet > >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4057 | TContigGapIter refIt = iter(referenceGaps,candidateViewPos-refStart); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:2477:41: required from ‘void seqan::dumpVariantsRealignBatchWrap(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCigars = StringSet > >; TReadCounts = String >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2477 | dumpVariantsRealignBatch(fragStoreGroup,readCigars, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2478 | readCounts,genomeID, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~ 2479 | groupStartCoord,groupStartPos,groupEndPos, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2480 | fileSNPs,fileIndels,options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:986:53: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 986 | dumpVariantsRealignBatchWrap(fragmentStore, readCigars, readCounts, genomeNames[i], startCoord, currentWindowBegin, currentWindowEnd, snpFileStream,indelFileStream,options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 77 | if (!open(seqFileIn, toCString(fileNameList[filecount]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 670 | if(result == CALLSNPS_GENOME_FAILED || !loadGenomes(genomes, genomeFileNameList, gIdStringToIdNumMap, genomeNames)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = const Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:689:35: required from ‘typename seqan::Iterator >::Type seqan::iter(const T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 689 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:669:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(const T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 669 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:451:22: required from ‘bool seqan::isGap(const Gaps >&, TPosition) [with TSequence = String, Alloc<> >; TGapAnchors = String, Alloc<> >; TPosition = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 451 | return isGap(iter(gaps, clippedViewPos)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:4418:72: required from ‘void seqan::dumpVariantsRealignBatch(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCounts = String >; TReadCigars = StringSet > >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4418 | ((indelConsens[candidateViewPos].i1 & 7) == 6 && isGap(referenceGaps, candidateViewPos-refStart))) // position in consensus is the same as in reference /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:2477:41: required from ‘void seqan::dumpVariantsRealignBatchWrap(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCigars = StringSet > >; TReadCounts = String >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2477 | dumpVariantsRealignBatch(fragStoreGroup,readCigars, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2478 | readCounts,genomeID, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~ 2479 | groupStartCoord,groupStartPos,groupEndPos, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2480 | fileSNPs,fileIndels,options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:986:53: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 986 | dumpVariantsRealignBatchWrap(fragmentStore, readCigars, readCounts, genomeNames[i], startCoord, currentWindowBegin, currentWindowEnd, snpFileStream,indelFileStream,options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 77 | if (!open(seqFileIn, toCString(fileNameList[filecount]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 670 | if(result == CALLSNPS_GENOME_FAILED || !loadGenomes(genomes, genomeFileNameList, gIdStringToIdNumMap, genomeNames)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 77 | if (!open(seqFileIn, toCString(fileNameList[filecount]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 670 | if(result == CALLSNPS_GENOME_FAILED || !loadGenomes(genomes, genomeFileNameList, gIdStringToIdNumMap, genomeNames)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 77 | if (!open(seqFileIn, toCString(fileNameList[filecount]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 670 | if(result == CALLSNPS_GENOME_FAILED || !loadGenomes(genomes, genomeFileNameList, gIdStringToIdNumMap, genomeNames)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 92%] Linking CXX executable ../../bin/snp_store cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/snp_store && /usr/bin/cmake -E cmake_link_script CMakeFiles/snp_store.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/snp_store.dir/snp_store.cpp.o -o ../../bin/snp_store -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:300:15, inlined from ‘__ct ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:87:23, inlined from ‘__ct_base ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:358:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:276:32, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:300:15, inlined from ‘__ct ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:87:23, inlined from ‘__ct_base ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:358:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 92%] Built target snp_store make -f apps/splazers/CMakeFiles/splazers.dir/build.make apps/splazers/CMakeFiles/splazers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/splazers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/splazers/CMakeFiles/splazers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/splazers/CMakeFiles/splazers.dir/build.make apps/splazers/CMakeFiles/splazers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 92%] Building CXX object apps/splazers/CMakeFiles/splazers.dir/splazers.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/splazers && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/splazers/CMakeFiles/splazers.dir/splazers.cpp.o -MF CMakeFiles/splazers.dir/splazers.cpp.o.d -o CMakeFiles/splazers.dir/splazers.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:28, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:676:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 676 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:704:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 704 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:730:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 730 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:748:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 748 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:770:45: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 770 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:51: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/outputFormat.h:126:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:513:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 513 | struct LessPairErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:604:11: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment, Alloc<> >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 340 | return TRevComp(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/outputFormat.h:1591:40: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1591 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 281 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:210:11: required from ‘bool seqan::loadReadsSam(TReadSet&, TNameSet&, TReadRegions&, const char*, TRazerSOptions&) [with TReadSet = StringSet, Alloc<> >, Owner > >; TNameSet = StringSet > >; TReadRegions = String > > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 210 | if (!open(file, fileName)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:190:21: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 190 | if (!loadReadsSam(readSet, readNames, readRegions, toCString(readFileNames[0]), options)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2543 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~ 2544 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2545 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~ 2546 | readSet,//readSetR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~ 2547 | forwardPatternsR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~ 2548 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~ 2549 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~ 2550 | LongestSuffix())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:666:22: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 666 | TGenomeInfix oriInf = inf; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:674:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 674 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestPrefix; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2591:20: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2591 | if (matchVerify( (*it).i2, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~ 2592 | infix(genome, (*it).i2.gBegin, maxEndPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2593 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~ 2594 | readSet, //readSetL /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~ 2595 | forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~ 2596 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~ 2597 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~ 2598 | LongestPrefix()) && /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:666:22: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 666 | TGenomeInfix oriInf = inf; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:674:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 674 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 763 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^ 764 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1430:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1979:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1979 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2125:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2125 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1430:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 140 | _host(std::forward(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment, Alloc<> >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 340 | return TRevComp(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/outputFormat.h:1591:40: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1591 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 281 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment, Alloc<> >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = Segment, Alloc<> >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:789:10: required from ‘TStream& seqan::operator<<(TStream&, const Segment&) [with TStream = VirtualStream >; THost = const String, Alloc<> >; TSpec = InfixSegment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 789 | write(it, source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/outputFormat.h:900:12: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 900 | file << reads[(*it).rseqNo]; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 281 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:98:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 98 | class ModifiedIterator > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >; typename Iterator >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:801:10: required from ‘TStream& seqan::operator<<(TStream&, const ModifiedString&) [with TStream = VirtualStream >; THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 801 | write(it, source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/outputFormat.h:1591:14: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1591 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 281 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:395:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 395 | data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2419:16: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2419 | TSwiftFinderL swiftFinderL(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:222: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, OneGappedShape>; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3041:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3041 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, onegappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, GappedShape > >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3043:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3043 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, gappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:68: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:674:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 674 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2543 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~ 2544 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2545 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~ 2546 | readSet,//readSetR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~ 2547 | forwardPatternsR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~ 2548 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 2549 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ 2550 | LongestSuffix())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, OneGappedShape>; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3074:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3074 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, onegappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, GappedShape > >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3076:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3076 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, gappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:395:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 395 | data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:671:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 671 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2187:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2187 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2190:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2190 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1430:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1430 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 763 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 764 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2198:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2198 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2201:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2201 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1876:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1876 | finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(const Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:910:21: required from ‘typename seqan::Parameter_::Type>::Type seqan::haystack(const TObject&) [with TObject = Finder, Alloc<> >, InfixSegment>, Swift > > >; typename Parameter_::Type>::Type = Segment, Alloc<> >, InfixSegment>; typename Haystack::Type = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 910 | return container(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1682:38: required from ‘seqan::Pair > >::Type> seqan::positionRange(const Finder >&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Tag >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1682 | int64_t textEnd = length(haystack(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1693:25: required from ‘seqan::Pair > >::Type> seqan::positionRange(Finder >&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Tag >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1693 | return positionRange(const_cast > const &>(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2489:26: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2489 | gPair = positionRange(swiftFinderL); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:606:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 606 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(const Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:910:21: required from ‘typename seqan::Parameter_::Type>::Type seqan::haystack(const TObject&) [with TObject = Finder, Alloc<> >, InfixSegment>, Swift > > >; typename Parameter_::Type>::Type = Segment, Alloc<> >, InfixSegment>; typename Haystack::Type = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 910 | return container(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1682:38: required from ‘seqan::Pair > >::Type> seqan::positionRange(const Finder >&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Tag >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1682 | int64_t textEnd = length(haystack(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1693:25: required from ‘seqan::Pair > >::Type> seqan::positionRange(Finder >&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Tag >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1693 | return positionRange(const_cast > const &>(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2489:26: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2489 | gPair = positionRange(swiftFinderL); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:606:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 606 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:675:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 675 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2543 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~ 2544 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2545 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~ 2546 | readSet,//readSetR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~ 2547 | forwardPatternsR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~ 2548 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 2549 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ 2550 | LongestSuffix())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1876:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1876 | finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1845:48: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1965 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1432:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1432 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 763 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 764 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = const Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 663 | TResult tmp(end(host(me), tag_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >; typename Iterator >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:801:10: required from ‘TStream& seqan::operator<<(TStream&, const ModifiedString&) [with TStream = VirtualStream >; THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 801 | write(it, source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/outputFormat.h:1591:14: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1591 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 281 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2383:33: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2383 | TReadSetL &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2384:33: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2384 | TReadSetR &readSetR = host(host(swiftPatternR)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, OneGappedShape>; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3041:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 3041 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, onegappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2384:33: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2384 | TReadSetR &readSetR = host(host(swiftPatternR)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, GappedShape > >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3043:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3043 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, gappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:652:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 652 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2543 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~ 2544 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2545 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~ 2546 | readSet,//readSetR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~ 2547 | forwardPatternsR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~ 2548 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~ 2549 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~ 2550 | LongestSuffix())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:675:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 675 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2543 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~ 2544 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2545 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~ 2546 | readSet,//readSetR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~ 2547 | forwardPatternsR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~ 2548 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 2549 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ 2550 | LongestSuffix())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:1717:14: required from ‘bool seqan::combineLeftRight(TMatch&, TMatch&, TRead&, TGenome&, RazerSOptions&, char, SwiftSemiGlobal) [with TMatch = ReadMatch; TRead = const Segment, Alloc<> >, InfixSegment>; TGenome = String, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1717 | appendValue(strL,genomeInfL); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2701:25: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2701 | !combineLeftRight(mRtmp,mLtmp,read,genome,options,orientation,TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:652:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 652 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:652:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 652 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2187:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2187 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:652:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 652 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2190:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2190 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1414:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1414 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 763 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^ 764 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1432:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1432 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 763 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 764 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 369 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1845:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1965 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 599 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:688:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 688 | while (find(myersFinderRev, myersPatternRev, maxScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2543 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~ 2544 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2545 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~ 2546 | readSet,//readSetR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~ 2547 | forwardPatternsR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~ 2548 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~ 2549 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ 2550 | LongestSuffix())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 369 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1845:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1965 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 599 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1437:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1437 | while (find(myersFinderRev, myersPatternRev, maxScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 763 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^ 764 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2701:25: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2701 | !combineLeftRight(mRtmp,mLtmp,read,genome,options,orientation,TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2701:25: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2701 | !combineLeftRight(mRtmp,mLtmp,read,genome,options,orientation,TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 135 | assignValue(*this, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:259:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:671:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 671 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:236:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:236:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:236:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:236:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 93%] Linking CXX executable ../../bin/splazers cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/splazers && /usr/bin/cmake -E cmake_link_script CMakeFiles/splazers.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/splazers.dir/splazers.cpp.o -o ../../bin/splazers -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 93%] Built target splazers make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/stellar /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 93%] Building CXX object apps/stellar/CMakeFiles/stellar.dir/stellar.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/stellar && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.4.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/stellar/CMakeFiles/stellar.dir/stellar.cpp.o -MF CMakeFiles/stellar.dir/stellar.cpp.o.d -o CMakeFiles/stellar.dir/stellar.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:24: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:25: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:30, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_types.h:155:32: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 155 | struct LessPos : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_types.h:207:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 207 | struct LessLength : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:127:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /usr/include/c++/14/bits/stl_function.h:117:12: note: 685 | mainWithOptions(options, String()); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 60 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 68 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 60 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 68 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 60 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 68 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 60 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 68 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 60 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 68 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 60 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 68 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:97: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_smart_pointer.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_allocator.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 467 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 467 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 467 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 467 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 467 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 467 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:190: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Dependent > >, IndexQGram, Tag > >; TSource = Index >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >, InfixSegment>, InfixSegment>*; TParam = const Segment >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment >, InfixSegment>, InfixSegment>; typename Value::Type = Segment >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment >, InfixSegment>, InfixSegment>; TValue2 = Segment >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet >, InfixSegment>, Owner<> >&; TSource = Segment >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment >, InfixSegment>, InfixSegment>; TIterator = char*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment >, InfixSegment>, InfixSegment>; TIterator = char*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment >, InfixSegment>, InfixSegment>; TIterator = char*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 647 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 647 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 647 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 647 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 647 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >, InfixSegment>*; TParam = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet >, InfixSegment>, Owner<> >&; TSource = Segment >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >, InfixSegment>*; TParam = const Segment >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet >, InfixSegment>, Owner<> >&; TSource = Segment >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment >, InfixSegment>, InfixSegment>; TIterator = char*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 647 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 95%] Linking CXX executable ../../bin/stellar cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/stellar && /usr/bin/cmake -E cmake_link_script CMakeFiles/stellar.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/stellar.dir/stellar.cpp.o -o ../../bin/stellar -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘pop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:915:22: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_goUp’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 95%] Built target stellar make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/tree_recon /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 95%] Building CXX object apps/tree_recon/CMakeFiles/tree_recon.dir/tree_recon.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/tree_recon && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/tree_recon/CMakeFiles/tree_recon.dir/tree_recon.cpp.o -MF CMakeFiles/tree_recon.dir/tree_recon.cpp.o.d -o CMakeFiles/tree_recon.dir/tree_recon.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon/tree_recon.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:37, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon/tree_recon.cpp:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon/tree_recon.cpp:18: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned long’, inlined from ‘readPhylipMatrix >, seqan::String >, seqan::Alloc >, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::String >&, seqan::String >, seqan::Alloc >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon/tree_recon.cpp:54:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘readPhylipMatrix >, seqan::String >, seqan::Alloc >, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::String >&, seqan::String >, seqan::Alloc >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const long unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned long const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 96%] Linking CXX executable ../../bin/tree_recon cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/tree_recon && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree_recon.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/tree_recon.dir/tree_recon.cpp.o -o ../../bin/tree_recon -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 96%] Built target tree_recon make -f apps/yara/CMakeFiles/yara_indexer.dir/build.make apps/yara/CMakeFiles/yara_indexer.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara/CMakeFiles/yara_indexer.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/yara/CMakeFiles/yara_indexer.dir/build.make apps/yara/CMakeFiles/yara_indexer.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 96%] Building CXX object apps/yara/CMakeFiles/yara_indexer.dir/indexer.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.9.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/yara/CMakeFiles/yara_indexer.dir/indexer.cpp.o -MF CMakeFiles/yara_indexer.dir/indexer.cpp.o.d -o CMakeFiles/yara_indexer.dir/indexer.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/store_seqs.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/store_seqs.h:209:34: required from ‘void trimSeqNames(SeqStore&) [with TSpec = void; TConfig = YaraContigsConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 209 | TSeqNameIt nameIt = begin(me.names[nameId], Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:201:21: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 201 | trimSeqNames(me.contigs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 195 | if (!open(me.contigsFile, toCString(me.options.contigsFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 195 | if (!open(me.contigsFile, toCString(me.options.contigsFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/store_seqs.h:209:34: required from ‘void trimSeqNames(SeqStore&) [with TSpec = void; TConfig = YaraContigsConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 209 | TSeqNameIt nameIt = begin(me.names[nameId], Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:201:21: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 201 | trimSeqNames(me.contigs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | if (!open(me.contigsFile, toCString(me.options.contigsFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 195 | if (!open(me.contigsFile, toCString(me.options.contigsFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 195 | if (!open(me.contigsFile, toCString(me.options.contigsFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, External > >; TString = String, Alloc<> >; TSpec = Owner > > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:186:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, False) [with TSA = String >, External > >; TText = StringSet, Alloc<> >, Owner > > > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 186 | _createSuffixArrayPipelining(sa, s, alg); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, External > >; TString = String, Alloc<> >; TSpec = Owner > > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:186:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, False) [with TSA = String >, External > >; TText = StringSet, Alloc<> >, Owner > > > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 186 | _createSuffixArrayPipelining(sa, s, alg); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 302 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:320:13: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:329:13: [ skipping 16 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ [ 98%] Linking CXX executable ../../bin/yara_indexer cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara && /usr/bin/cmake -E cmake_link_script CMakeFiles/yara_indexer.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/yara_indexer.dir/indexer.cpp.o -o ../../bin/yara_indexer -lrt -lz -lbz2 In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘operator++.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:345:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:280:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:290:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign.constprop.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘assign.constprop.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 98%] Built target yara_indexer make -f apps/yara/CMakeFiles/yara_mapper.dir/build.make apps/yara/CMakeFiles/yara_mapper.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara/CMakeFiles/yara_mapper.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/yara/CMakeFiles/yara_mapper.dir/build.make apps/yara/CMakeFiles/yara_mapper.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 98%] Building CXX object apps/yara/CMakeFiles/yara_mapper.dir/mapper.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.9.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/yara/CMakeFiles/yara_mapper.dir/mapper.cpp.o -MF CMakeFiles/yara_mapper.dir/mapper.cpp.o.d -o CMakeFiles/yara_mapper.dir/mapper.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/random:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:51: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/store_seqs.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:69: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In function ‘void rankMatches(Mapper&, const TReadSeqs&)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/backward/binders.h:172:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/backward/binders.h:172:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/backward/binders.h:172:5: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1326 | rankMatches(me, readSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1328 | verifyMatches(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:97: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:140: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_smart_pointer.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_allocator.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:57: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:205:36: required from ‘typename seqan::Parameter_::Type seqan::cargo(const ModifiedString >&) [with THost = String >, Alloc<> >; TPositions = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 205 | return _toParameter(me._cargo); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:309:23: required from ‘bool seqan::empty(const ModifiedString >&) [with THost = String >, Alloc<> >; TPositions = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 309 | return empty(cargo(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:858:18: required from ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 858 | if (empty(matches)) return TMatchesSize(0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1326 | rankMatches(me, readSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >, Alloc<> >; TSpec = SuffixSegment; typename Pointer_ >::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | me.data_host = _toPointer(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1109 | setHost(me.matesSetByCoord, me.matesByCoord); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >, Alloc<> >; TSpec = SuffixSegment; typename Pointer_ >::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 296 | me.data_host = _toPointer(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1109 | setHost(me.matesSetByCoord, me.matesByCoord); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >, Alloc<> >; TSpec = SuffixSegment; typename Pointer_ >::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 296 | me.data_host = _toPointer(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1109 | setHost(me.matesSetByCoord, me.matesByCoord); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >, Alloc<> >; TSpec = SuffixSegment; typename Pointer_ >::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 296 | me.data_host = _toPointer(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1109 | setHost(me.matesSetByCoord, me.matesByCoord); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/file_prefetched.h:151:13: required from ‘bool seqan::open(PrefetchedFile >&, const char*) [with TFile = FormattedFile, Tag >; TRecords = SeqStore >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 151 | if (open(me.file, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:408:14: required from ‘void _openReadsImpl(Mapper&, SingleEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; SingleEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 408 | if (!open(me.readsFile, toCString(me.options.readsFile.i1))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:402:19: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, Owner > >, PrefixSegment>; TIterator = Iter, Alloc<> >, Owner > >, CountingIteratorImpl_ > >; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:244:37: required from ‘void seqan::iterate(TContainer&, TFunctor, const Tag&, Parallel) [with TContainer = Segment, Alloc<> >, Owner > >, PrefixSegment>; TFunctor = ReadsClassifier, Tag, Tag, unsigned char, unsigned int, unsigned int, MMap<>, 3> > >; TIterTag = Rooted_; Parallel = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 244 | TIter it = begin(c, iterTag) + splitter[i]; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_classifier.h:114:12: required from ‘void _classifyReadsImpl(ReadsClassifier&, Strata) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | iterate(pairs, me, Rooted(), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_classifier.h:76:27: required from ‘ReadsClassifier::ReadsClassifier(TReadsContext&, THits&, const TSeeds&, const Options&) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadsContext = ReadsContext, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THits = seqan::String >, seqan::Alloc<> >; TSeeds = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >, seqan::Segment, seqan::Alloc<> >, seqan::Owner > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 76 | _classifyReadsImpl(*this, typename TConfig::TStrategy()); //, typename TConfig::TAnchoring()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:656:17: required from ‘void classifyReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 656 | TClassifier classifier(me.ctx, me.hits[0], me.seeds[0], me.options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1288:18: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1288 | classifyReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(StringSet >&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 279 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; TKeyGetter = Getter >, const Tag >; TMaxKey = long unsigned int; TThreading = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 182 | forEach(host(me), TCounter(stringSetLimits(me), nextKey), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1110 | bucket(me.matesSetByCoord, Getter(), getReadsCount(me.reads.seqs), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(StringSet >&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 279 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; TKeyGetter = Getter >, const Tag >; TMaxKey = long unsigned int; TThreading = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 182 | forEach(host(me), TCounter(stringSetLimits(me), nextKey), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1110 | bucket(me.matesSetByCoord, Getter(), getReadsCount(me.reads.seqs), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(StringSet >&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 279 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; TKeyGetter = Getter >, const Tag >; TMaxKey = long unsigned int; TThreading = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 182 | forEach(host(me), TCounter(stringSetLimits(me), nextKey), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1110 | bucket(me.matesSetByCoord, Getter(), getReadsCount(me.reads.seqs), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(StringSet >&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 279 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; TKeyGetter = Getter >, const Tag >; TMaxKey = long unsigned int; TThreading = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 182 | forEach(host(me), TCounter(stringSetLimits(me), nextKey), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1110 | bucket(me.matesSetByCoord, Getter(), getReadsCount(me.reads.seqs), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/file_prefetched.h:151:13: required from ‘bool seqan::open(PrefetchedFile >&, const char*) [with TFile = FormattedFile, Tag >; TRecords = SeqStore >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 151 | if (open(me.file, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:408:14: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, Owner > >, PrefixSegment>; typename Iterator >::Type = Iter, Alloc<> >, Owner > >, PrefixSegment>, AdaptorIterator, Alloc<> >, Owner > >, CountingIteratorImpl_ > >, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, Owner > >, PrefixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, Owner > >, PrefixSegment>, AdaptorIterator, Alloc<> >, Owner > >, CountingIteratorImpl_ > >, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, Owner > >, PrefixSegment>; typename Iterator >::Type = Iter, Alloc<> >, Owner > >, PrefixSegment>, AdaptorIterator, Alloc<> >, Owner > >, CountingIteratorImpl_ > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:244:24: required from ‘void seqan::iterate(TContainer&, TFunctor, const Tag&, Parallel) [with TContainer = Segment, Alloc<> >, Owner > >, PrefixSegment>; TFunctor = ReadsClassifier, Tag, Tag, unsigned char, unsigned int, unsigned int, MMap<>, 3> > >; TIterTag = Rooted_; Parallel = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 244 | TIter it = begin(c, iterTag) + splitter[i]; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_classifier.h:114:12: required from ‘void _classifyReadsImpl(ReadsClassifier&, Strata) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | iterate(pairs, me, Rooted(), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_classifier.h:76:27: required from ‘ReadsClassifier::ReadsClassifier(TReadsContext&, THits&, const TSeeds&, const Options&) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadsContext = ReadsContext, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THits = seqan::String >, seqan::Alloc<> >; TSeeds = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >, seqan::Segment, seqan::Alloc<> >, seqan::Owner > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 76 | _classifyReadsImpl(*this, typename TConfig::TStrategy()); //, typename TConfig::TAnchoring()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:656:17: required from ‘void classifyReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 656 | TClassifier classifier(me.ctx, me.hits[0], me.seeds[0], me.options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1288:18: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/write_sam.h:114:14: required from ‘void seqan::write(TTarget&, const BamHeader&, const BamIOContext&, const Sam&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TNameStore = StringSet >, Owner > > >; TNameStoreCache = NameStoreCache >, Owner > > >, String > >; TStorageSpec = Dependent >; BamHeader = String; Sam = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | write(target, contigNames(context)[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:293:14: required from ‘void seqan::write(TTarget&, const BamHeader&, BamIOContext&, const TagSelector&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TNameStore = StringSet >, Owner > > >; TNameStoreCache = NameStoreCache >, Owner > > >, String > >; TStorageSpec = Dependent >; TTagList = TagList >; BamHeader = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 293 | write(target, header, context, TFormat()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:295:14: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/file_prefetched.h:151:13: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const StringSet, Alloc<> >, Owner > >; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, Owner > >, PrefixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: required from ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, Owner > >, PrefixSegment>; TIterator = Iter, Alloc<> >, Owner > >, CountingIteratorImpl_ > >; TSpec = Tag; TIntegral = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 577 | return Iter >(container(left), hostIterator(left) + right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:244:37: required from ‘void seqan::iterate(TContainer&, TFunctor, const Tag&, Parallel) [with TContainer = Segment, Alloc<> >, Owner > >, PrefixSegment>; TFunctor = ReadsClassifier, Tag, Tag, unsigned char, unsigned int, unsigned int, MMap<>, 3> > >; TIterTag = Rooted_; Parallel = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 244 | TIter it = begin(c, iterTag) + splitter[i]; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_classifier.h:114:12: required from ‘void _classifyReadsImpl(ReadsClassifier&, Strata) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | iterate(pairs, me, Rooted(), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_classifier.h:76:27: required from ‘ReadsClassifier::ReadsClassifier(TReadsContext&, THits&, const TSeeds&, const Options&) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadsContext = ReadsContext, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THits = seqan::String >, seqan::Alloc<> >; TSeeds = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >, seqan::Segment, seqan::Alloc<> >, seqan::Owner > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 76 | _classifyReadsImpl(*this, typename TConfig::TStrategy()); //, typename TConfig::TAnchoring()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:656:17: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:216:27: required from ‘void seqan::setCargo(ModifiedString >&, typename Parameter_::Type) [with THost = String >, Alloc<> >; TPositions = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 216 | me._cargo = _toPointer(_cargo); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:357:13: required from ‘typename seqan::Infix > >::Type seqan::infix(ModifiedString >&, TPosBegin, TPosEnd) [with THost = String >, Alloc<> >; TPositions = String >; TPosBegin = long unsigned int; TPosEnd = long unsigned int; typename Infix > >::Type = ModifiedString >, Alloc<> >, ModPos >, InfixSegment> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 357 | setCargo(other, infix(cargo(me), pos_begin, pos_end)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:649:17: required from ‘typename seqan::Infix::Type seqan::infixWithLength(T&&, TPosBegin, TSize) [with T = ModifiedString >, Alloc<> >, ModPos > > >; TPosBegin = long unsigned int; TSize = long unsigned int; typename Infix::Type = ModifiedString >, Alloc<> >, ModPos >, InfixSegment> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 649 | return infix(t, pos_begin, pos_begin + length); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:489:27: required from ‘typename seqan::InfixOnValue::Type seqan::value(const StringSet >&, TPos) [with THost = ModifiedString >, Alloc<> >, ModPos > > >; TSpec = ModifiedString >, Alloc<> >, ModPos > > >; TPos = long unsigned int; typename InfixOnValue::Type = const ModifiedString >, Alloc<> >, ModPos >, InfixSegment> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 489 | return infixWithLength(host(me), me.positions[pos], me.limits[pos + 1] - me.limits[pos]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:215:17: required from ‘typename seqan::Reference > > >::Type seqan::value(const Iter > >&) [with TContainer = const StringSet >, Alloc<> >, ModPos > > >, Segment >, Alloc<> >, ModPos > > >, InfixSegment> >; typename Reference > > >::Type = const ModifiedString >, Alloc<> >, ModPos >, InfixSegment> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 215 | return value(container(me), position(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:885:53: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1397:14: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1397 | openReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h: In instantiation of ‘void setQual(seqan::BamAlignmentRecord&, const TString&) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:455:12: required from ‘void _fillReadSeqQual(MatchesWriter&, TReadSeqId) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadSeqId = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 455 | setQual(me.record, me.reads.seqs[readSeqId]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:305:21: required from ‘void _writeMappedRead(MatchesWriter&, TReadId, const TMatch&, SingleEnd) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadId = long unsigned int; TMatch = Match >; SingleEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _fillReadSeqQual(me, getReadSeqId(primary, me.reads.seqs)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:236:25: required from ‘void _writeMatchesImpl(MatchesWriter&, const TMatchIt&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TMatchIt = seqan::Iter >, seqan::Alloc<> >, seqan::ModPos > > >, seqan::ModPos > > >, seqan::CountingIteratorImpl_ > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 236 | _writeMappedRead(me, position(it, me.primaryMatches), primary, typename Traits::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:102:26: required from ‘void MatchesWriter::operator()(const TIterator&) [with TIterator = seqan::Iter >, seqan::Alloc<> >, seqan::ModPos > > >, seqan::ModPos > > >, seqan::CountingIteratorImpl_ > >; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 102 | _writeMatchesImpl(*this, it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:248:14: required from ‘void seqan::iterate(TContainer&, TFunctor, const Tag&, Parallel) [with TContainer = const ModifiedString >, Alloc<> >, ModPos > > >, ModPos > > >; TFunctor = MatchesWriter, Tag, Tag, unsigned char, unsigned int, unsigned int, MMap<>, 3> > >; TIterTag = Standard_; Parallel = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | f(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:96:16: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:164:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 164 | TQualities qual(string); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:81: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h: In instantiation of ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | if (!_extendLeft(extender, haystackLeft, needleLeft, matchBegin, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 216 | extend(me.extender, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~ 217 | readSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~ 218 | contigBegin, contigEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~ 219 | getValueI1(readPos), getValueI2(readPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 | hitErrors, maxErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~ 221 | me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 112 | _extendHitImpl(*this, hitsIt, typename Traits::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:248:14: required from ‘void seqan::iterate(TContainer&, TFunctor, const Tag&, Parallel) [with TContainer = const String >, Alloc<> >; TFunctor = HitsExtender, Tag, Tag, unsigned char, unsigned int, unsigned int, MMap<>, 3> > >; TIterTag = Standard_; Parallel = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | f(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:134:12: required from ‘void _extendHitsImpl(HitsExtender&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 134 | iterate(me.hits, me, Standard(), typename Traits::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:106:24: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:220:25: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 220 | TNeedleInfixRev needleInfixRev(needleInfix); | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:221:27: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 221 | THaystackInfixRev haystackInfixRev(haystackInfix); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:241:21: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 241 | TNeedleInfixRev needleInfixRev(needleInfix); | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:242:23: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 242 | THaystackInfixRev haystackInfixRev(haystackInfix); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h: In instantiation of ‘bool _extendRight(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:429:26: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 429 | if (!_extendRight(extender, haystackRight, needleRight, matchEnd, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 216 | extend(me.extender, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~ 217 | readSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~ 218 | contigBegin, contigEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~ 219 | getValueI1(readPos), getValueI2(readPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 | hitErrors, maxErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~ 221 | me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 112 | _extendHitImpl(*this, hitsIt, typename Traits::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:248:14: required from ‘void seqan::iterate(TContainer&, TFunctor, const Tag&, Parallel) [with TContainer = const String >, Alloc<> >; TFunctor = HitsExtender, Tag, Tag, unsigned char, unsigned int, unsigned int, MMap<>, 3> > >; TIterTag = Standard_; Parallel = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 248 | f(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:134:12: required from ‘void _extendHitsImpl(HitsExtender&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 134 | iterate(me.hits, me, Standard(), typename Traits::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:106:24: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:311:20: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 311 | THaystackInfix haystackPrefix(haystackInfix); | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:312:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 312 | TNeedleInfix needlePrefix(needleInfix); | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/write_sam.h:114:14: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:402:19: required from ‘void openReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 402 | _openReadsImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1397:14: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1397 | openReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:164:16: required from ‘void setQual(seqan::BamAlignmentRecord&, const TString&) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 164 | TQualities qual(string); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:455:12: required from ‘void _fillReadSeqQual(MatchesWriter&, TReadSeqId) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadSeqId = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 455 | setQual(me.record, me.reads.seqs[readSeqId]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:305:21: required from ‘void _writeMappedRead(MatchesWriter&, TReadId, const TMatch&, SingleEnd) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadId = long unsigned int; TMatch = Match >; SingleEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _fillReadSeqQual(me, getReadSeqId(primary, me.reads.seqs)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:236:25: required from ‘void _writeMatchesImpl(MatchesWriter&, const TMatchIt&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TMatchIt = seqan::Iter >, seqan::Alloc<> >, seqan::ModPos > > >, seqan::ModPos > > >, seqan::CountingIteratorImpl_ > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 236 | _writeMappedRead(me, position(it, me.primaryMatches), primary, typename Traits::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:102:26: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:220:25: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 220 | TNeedleInfixRev needleInfixRev(needleInfix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | if (!_extendLeft(extender, haystackLeft, needleLeft, matchBegin, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 216 | extend(me.extender, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~ 217 | readSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 218 | contigBegin, contigEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~ 219 | getValueI1(readPos), getValueI2(readPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 | hitErrors, maxErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~ 221 | me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 112 | _extendHitImpl(*this, hitsIt, typename Traits::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:248:14: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Packed > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Packed > >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:221:27: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 221 | THaystackInfixRev haystackInfixRev(haystackInfix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | if (!_extendLeft(extender, haystackLeft, needleLeft, matchBegin, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 216 | extend(me.extender, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~ 217 | readSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 218 | contigBegin, contigEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~ 219 | getValueI1(readPos), getValueI2(readPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 | hitErrors, maxErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~ 221 | me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 112 | _extendHitImpl(*this, hitsIt, typename Traits::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:248:14: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Packed > >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:243:17: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 243 | TFinderLeft finder(haystackInfixRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | if (!_extendLeft(extender, haystackLeft, needleLeft, matchBegin, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 216 | extend(me.extender, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~ 217 | readSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 218 | contigBegin, contigEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~ 219 | getValueI1(readPos), getValueI2(readPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 | hitErrors, maxErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~ 221 | me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:112:23: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Packed > >, InfixSegment>; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Packed > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; typename RemoveReference::Type = Segment, Packed > >, InfixSegment>; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:317:18: required from ‘bool _extendRight(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 317 | TFinderRight finder(haystackPrefix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:429:26: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 429 | if (!_extendRight(extender, haystackRight, needleRight, matchEnd, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 216 | extend(me.extender, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~ 217 | readSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 218 | contigBegin, contigEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~ 219 | getValueI1(readPos), getValueI2(readPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 | hitErrors, maxErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~ 221 | me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:112:23: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Packed > >, InfixSegment>; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Packed > >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Packed > >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:243:17: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 243 | TFinderLeft finder(haystackInfixRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | if (!_extendLeft(extender, haystackLeft, needleLeft, matchBegin, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Packed > >, InfixSegment>*; TParam = const Segment, Packed > >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Packed > >, InfixSegment>, Tag >; TValue = Segment, Packed > >, InfixSegment>; typename Value::Type = Segment, Packed > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Packed > >, InfixSegment>; TValue2 = const Segment, Packed > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Packed > >, InfixSegment>; TSource = Segment, Packed > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 135 | assignValue(*this, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:175:9: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 135 | assignValue(*this, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:175:9: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Packed > >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Packed > >, InfixSegment>; TIterator = Iter, Packed > >, Packed > >; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Packed > >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Packed > >, InfixSegment>; TIterator = Iter, Packed > >, Packed > >; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Packed > >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Packed > >, InfixSegment>; TIterator = Iter, Packed > >, Packed > >; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:46: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Packed > >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Packed > >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_interface.h:430:24: required from ‘void seqan::goEnd(TIterator&) [with TIterator = ModifiedIterator, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 430 | goEnd(it, container(it)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:737:10: required from ‘void seqan::goEnd(Finder&) [with THaystack = ModifiedString, Packed > >, InfixSegment>, Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 737 | goEnd(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1537:18: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1537 | goEnd(finder); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1646:16: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder, Packed > >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1646 | return find(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:246:16: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 246 | while (find(finder, needleInfixRev, extender.patternLeft, -static_cast(remainingErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:413:25: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Packed > >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Packed > >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:989:66: required from ‘bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = Segment, Alloc<> >, InfixSegment>; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 989 | typename Size::Type const columns = length(container(finder)) + state.leftClip; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1181:44: required from ‘bool seqan::_stateInit(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = Segment, Alloc<> >, InfixSegment>; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1181 | return _patternInitSmallStateBanded(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1535:24: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = Segment, Alloc<> >, InfixSegment>; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1535 | if (!_stateInit(finder, needle, state)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1646:16: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder, Packed > >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = Segment, Alloc<> >, InfixSegment>; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1646 | return find(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:320:16: required from ‘bool _extendRight(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 320 | while (find(finder, needlePrefix, extender.patternRight, -static_cast(remainingErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:429:26: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:993:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 993 | TConstSeqVIterator itV = begin(seqV, Rooted()) + _max(0, _min(seqVlength - 1, -lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:612:32: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 612 | _computeHammingDistance(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoringScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 613 | dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:994:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 994 | TConstSeqVIterator itVEnd = begin(seqV, Rooted()) + _min(seqVlength - 1, lowerDiagonal(band) + seqHlength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:612:32: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 612 | _computeHammingDistance(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoringScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 613 | dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Packed > >, InfixSegment>; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Packed > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; typename RemoveReference::Type = Segment, Packed > >, InfixSegment>; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:45: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Packed > >, InfixSegment>; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Packed > >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:381:19: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = SimpleType; TSeqVValue = SimpleType; TSeqVIterator = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TScoringScheme = Score >; TDPCell = DPCell_ >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 381 | TSeqVIterator iter = seqBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:891:38: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 891 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 892 | sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 893 | sequenceEntryForScore(scoringScheme, seqV, 0), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 894 | seqVBegin, seqVEnd, scoringScheme, cacheDiag, cacheVert, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 895 | MetaColumnDescriptor(), dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:287:63: required from ‘void seqan::compare_(Lexical&, TLeft&, TRight&) [with TSpec = long unsigned int; TLeft = const ModifiedString, Packed > >, InfixSegment>, Tag >; TRight = const ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | typename Iterator::Type right_it = begin(right, Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:323:13: required from ‘void seqan::compare(Lexical&, const TLeft&, const TRight&) [with TSpec = long unsigned int; TLeft = ModifiedString, Packed > >, InfixSegment>, Tag >; TRight = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 323 | compare_(lexical, left, right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:170:16: required from ‘seqan::Lexical::Lexical(const TLeft&, const TRight&) [with TLeft = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TRight = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 170 | compare(*this, left, right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:750:38: required from ‘typename seqan::Size::Type seqan::lcpLength(const TLeft&, const TRight&) [with TLeft = ModifiedString, Packed > >, InfixSegment>, Tag >; TRight = ModifiedString, Alloc<> >, InfixSegment>, Tag >; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 750 | typename Comparator::Type _lex(left, right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:222:24: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:509:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWise&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWise = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 509 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_verifier.h:112:39: required from ‘void verify(Verifier >&, const TNeedle&, THaystackPos, THaystackPos, TErrors, TErrors, TDelegate&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TDelegate = AnchorsVerifier, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 112 | int errors = _setUpAndRunAlignment(me.dpContext, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 113 | me.traceSegments, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~ 114 | me.dpScoutState, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~ 115 | source(contigGaps), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~ 116 | source(readGaps), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~ 117 | Score(0, -1000, -999, -1001), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 | TAlignConfig2()) / -999; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_verifier.h:193:11: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:510:37: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWise&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWise = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 510 | TConstSeqVIterator seqVEnd = end(seqV, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_verifier.h:112:39: required from ‘void verify(Verifier >&, const TNeedle&, THaystackPos, THaystackPos, TErrors, TErrors, TDelegate&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TDelegate = AnchorsVerifier, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 112 | int errors = _setUpAndRunAlignment(me.dpContext, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 113 | me.traceSegments, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~ 114 | me.dpScoutState, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~ 115 | source(contigGaps), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~ 116 | source(readGaps), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~ 117 | Score(0, -1000, -999, -1001), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 | TAlignConfig2()) / -999; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_verifier.h:193:11: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:287:63: required from ‘void seqan::compare_(Lexical&, TLeft&, TRight&) [with TSpec = long unsigned int; TLeft = const ModifiedString, Packed > >, InfixSegment>, Tag >; TRight = const ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | typename Iterator::Type right_it = begin(right, Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:323:13: required from ‘void seqan::compare(Lexical&, const TLeft&, const TRight&) [with TSpec = long unsigned int; TLeft = ModifiedString, Packed > >, InfixSegment>, Tag >; TRight = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 323 | compare_(lexical, left, right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:170:16: required from ‘seqan::Lexical::Lexical(const TLeft&, const TRight&) [with TLeft = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TRight = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 170 | compare(*this, left, right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:750:38: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:503:103: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(const ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 503 | typename Iterator const, Tag const >::Type temp_(begin(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:994:21: required from ‘bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 994 | ndlEnd = end(needle, Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1181:44: required from ‘bool seqan::_stateInit(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1181 | return _patternInitSmallStateBanded(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1535:24: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1535 | if (!_stateInit(finder, needle, state)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1646:16: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:382:27: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = SimpleType; TSeqVValue = SimpleType; TSeqVIterator = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TScoringScheme = Score >; TDPCell = DPCell_ >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 382 | for (; iter != seqEnd - 1; ++iter) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:453:18: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = SimpleType; TSeqVValue = SimpleType; TSeqVIterator = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TScoringScheme = Score >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 453 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqHValue, seqVValue, seqBegin, seqEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 454 | scoringScheme, cacheDiag, cacheVert, TColumnDescriptor{}, TDPProfile{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:515:18: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWise&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWise = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 515 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 516 | sequenceEntryForScore(scoringScheme, seqH, 0), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 517 | sequenceEntryForScore(scoringScheme, seqV, 0), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 518 | seqVBegin, seqVEnd, scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 519 | MetaColumnDescriptor(), dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_verifier.h:112:39: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ [100%] Linking CXX executable ../../bin/yara_mapper cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara && /usr/bin/cmake -E cmake_link_script CMakeFiles/yara_mapper.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/yara_mapper.dir/mapper.cpp.o -o ../../bin/yara_mapper -lrt -lz -lbz2 In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [100%] Built target yara_mapper make[1]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles 0 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.LuzvkF + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x '!=' / ']' + rm -rf /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x ++ dirname /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd seqan-seqan-v2.4.0 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x 'INSTALL=/usr/bin/install -p' -C build/library make: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library' /usr/bin/cmake -S/builddir/build/BUILD/seqan-seqan-v2.4.0 -B/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library/CMakeFiles /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[1]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library' make[1]: Nothing to be done for 'preinstall'. make[1]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2/README.rst -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2/CHANGELOG.rst -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/lib64/pkgconfig/seqan-2.pc -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/lib64/cmake/seqan2/seqan-config.cmake -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/align_base.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/align_cols.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/align_config.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/align_interface_wrapper.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/align_iterator_base.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/align_metafunctions.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/align_traceback.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/aligned_sequence_concept.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/alignment_algorithm_tags.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/alignment_operations.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_algorithm_impl.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_align_simd_helper.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_band.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_cell.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_cell_affine.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_cell_dynamic.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_cell_linear.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_context.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_formula.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_formula_affine.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_formula_dynamic.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_formula_linear.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_matrix.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_matrix_navigator.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_matrix_navigator_score_matrix.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/align/dp_matrix_navigator_score_matrix_sparse.h -- Installing: 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-- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/tabix_io/tabix_index_tbi.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/translation.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/translation/translation.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/translation/translation_tables.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/ucsc_io.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/ucsc_io/ucsc_file.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/ucsc_io/ucsc_io.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/include/seqan2/seqan/ucsc_io/ucsc_record.h -- Installing: 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directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library' + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x 'INSTALL=/usr/bin/install -p' -C build/Release make: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/cmake -S/builddir/build/BUILD/seqan-seqan-v2.4.0 -B/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && 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'/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools/CMakeFiles/bisar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/bs_tools/CMakeFiles/bisar.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 1%] Built target bisar /usr/bin/make -f 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'/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/bs_tools/CMakeFiles/four2three.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Built target four2three /usr/bin/make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/dfi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/dfi/CMakeFiles/dfi.dir/build.make 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'/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/fiona/CMakeFiles/compute_gain.dir/build.make apps/fiona/CMakeFiles/compute_gain.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/fiona/CMakeFiles/compute_gain.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 6%] Built target compute_gain /usr/bin/make -f apps/fiona/CMakeFiles/fiona.dir/build.make apps/fiona/CMakeFiles/fiona.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona/CMakeFiles/fiona.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/fiona/CMakeFiles/fiona.dir/build.make apps/fiona/CMakeFiles/fiona.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/fiona/CMakeFiles/fiona.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 7%] Built target fiona /usr/bin/make -f apps/fiona/CMakeFiles/fiona_illumina.dir/build.make apps/fiona/CMakeFiles/fiona_illumina.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona/CMakeFiles/fiona_illumina.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/fiona/CMakeFiles/fiona_illumina.dir/build.make apps/fiona/CMakeFiles/fiona_illumina.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/fiona/CMakeFiles/fiona_illumina.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 9%] Built target fiona_illumina /usr/bin/make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 10%] Built target fx_bam_coverage /usr/bin/make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 12%] Built target fx_fastq_stats /usr/bin/make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf/CMakeFiles/gustaf.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/gustaf/CMakeFiles/gustaf.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 14%] Built target gustaf /usr/bin/make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 15%] Built target gustaf_mate_joining /usr/bin/make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/insegt /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/insegt/CMakeFiles/insegt.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 17%] Built target insegt /usr/bin/make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_sim.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_sim.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 25%] Built target mason_sim /usr/bin/make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_genome.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 26%] Built target mason_genome /usr/bin/make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_methylation.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 28%] Built target mason_methylation /usr/bin/make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 29%] Built target mason_frag_sequencing /usr/bin/make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_variator.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 31%] Built target mason_variator /usr/bin/make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_materializer.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 31%] Built target mason_materializer /usr/bin/make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_simulator.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 32%] Built target mason_simulator /usr/bin/make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_splicing.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 34%] Built target mason_splicing /usr/bin/make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_tests.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 35%] Built target mason_tests /usr/bin/make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers/CMakeFiles/micro_razers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/micro_razers/CMakeFiles/micro_razers.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 37%] Built target micro_razers /usr/bin/make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 39%] Built target roi_plot_thumbnails /usr/bin/make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi/CMakeFiles/bam2roi.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/ngs_roi/CMakeFiles/bam2roi.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 42%] Built target bam2roi /usr/bin/make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 45%] Built target roi_feature_projection /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Built target pair_align_global_1111 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Built target pair_align_lcs /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_local.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Built target pair_align_local /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 48%] Built target pair_align_global_0000 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 48%] Built target pair_align_global_0001 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Built target pair_align_global_0010 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Built target pair_align_global_0011 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 51%] Built target pair_align_global_0100 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 51%] Built target pair_align_global_0101 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Built target pair_align_global_0110 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Built target pair_align_global_0111 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Built target pair_align_global_1000 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 54%] Built target pair_align_global_1001 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 54%] Built target pair_align_global_1010 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 56%] Built target pair_align_global_1011 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 56%] Built target pair_align_global_1100 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 57%] Built target pair_align_global_1101 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 57%] Built target pair_align_global_1110 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 59%] Built target pair_align_lib /usr/bin/make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/CMakeFiles/pair_align.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/CMakeFiles/pair_align.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 60%] Built target pair_align /usr/bin/make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/param_chooser/CMakeFiles/param_chooser.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 62%] Built target param_chooser /usr/bin/make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 64%] Built target test_funcs_param_chooser /usr/bin/make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 65%] Built target rabema_prepare_sam /usr/bin/make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 67%] Built target rabema_build_gold_standard /usr/bin/make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_evaluate.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 68%] Built target rabema_evaluate /usr/bin/make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_do_search.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 70%] Built target rabema_do_search /usr/bin/make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/razers/CMakeFiles/razers.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 71%] Built target razers /usr/bin/make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/razers3/CMakeFiles/razers3.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 73%] Built target razers3 /usr/bin/make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 75%] Built target razers3_simulate_reads /usr/bin/make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/razers3/CMakeFiles/razers3_quality2prob.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 76%] Built target razers3_quality2prob /usr/bin/make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rep_sep /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/rep_sep/CMakeFiles/rep_sep.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 78%] Built target rep_sep /usr/bin/make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/sak/CMakeFiles/sak.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 79%] Built target sak /usr/bin/make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sam2matrix /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/sam2matrix/CMakeFiles/sam2matrix.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 81%] Built target sam2matrix /usr/bin/make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/samcat /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/samcat/CMakeFiles/samcat.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 81%] Built target samcat /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/searchjoin/CMakeFiles/s4_search.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 82%] Built target s4_search /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/searchjoin/CMakeFiles/s4_join.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 84%] Built target s4_join /usr/bin/make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqan_tcoffee /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 85%] Built target seqan_tcoffee /usr/bin/make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/seqcons2/CMakeFiles/seqcons2.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 89%] Built target seqcons2 /usr/bin/make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sgip /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/sgip/CMakeFiles/sgip.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 90%] Built target sgip /usr/bin/make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/snp_store /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/snp_store/CMakeFiles/snp_store.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 92%] Built target snp_store /usr/bin/make -f apps/splazers/CMakeFiles/splazers.dir/build.make apps/splazers/CMakeFiles/splazers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/splazers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/splazers/CMakeFiles/splazers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/splazers/CMakeFiles/splazers.dir/build.make apps/splazers/CMakeFiles/splazers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/splazers/CMakeFiles/splazers.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 93%] Built target splazers /usr/bin/make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/stellar /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/stellar/CMakeFiles/stellar.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 95%] Built target stellar /usr/bin/make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/tree_recon /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/tree_recon/CMakeFiles/tree_recon.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 96%] Built target tree_recon /usr/bin/make -f apps/yara/CMakeFiles/yara_indexer.dir/build.make apps/yara/CMakeFiles/yara_indexer.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara/CMakeFiles/yara_indexer.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/yara/CMakeFiles/yara_indexer.dir/build.make apps/yara/CMakeFiles/yara_indexer.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/yara/CMakeFiles/yara_indexer.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 98%] Built target yara_indexer /usr/bin/make -f apps/yara/CMakeFiles/yara_mapper.dir/build.make apps/yara/CMakeFiles/yara_mapper.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara/CMakeFiles/yara_mapper.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/yara/CMakeFiles/yara_mapper.dir/build.make apps/yara/CMakeFiles/yara_mapper.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/yara/CMakeFiles/yara_mapper.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [100%] Built target yara_mapper make[1]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[1]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[1]: Nothing to be done for 'preinstall'. make[1]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/alf -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/libexec/seqan2/examples/alf/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/libexec/seqan2/examples/alf/README -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/libexec/seqan2/examples/alf/example/small.fasta -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/bisar -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/casbar -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/four2three -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/libexec/seqan2/examples/bs_tools/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/libexec/seqan2/examples/bs_tools/README -- Installing: 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'/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/cmake -S/builddir/build/BUILD/seqan-seqan-v2.4.0 -B/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/gmake -f CMakeFiles/Makefile2 sak_doc gmake[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/cmake -S/builddir/build/BUILD/seqan-seqan-v2.4.0 -B/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles 2 /usr/bin/gmake -f CMakeFiles/Makefile2 apps/sak/CMakeFiles/sak_doc.dir/all gmake[3]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/gmake -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend gmake[4]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles/seqan_library.dir/DependInfo.cmake "--color=" gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/gmake -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/build gmake[4]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' gmake[4]: Nothing to be done for 'CMakeFiles/seqan_library.dir/build'. gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 0%] Built target seqan_library /usr/bin/gmake -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend gmake[4]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake "--color=" gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/gmake -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build gmake[4]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' gmake[4]: Nothing to be done for 'apps/sak/CMakeFiles/sak.dir/build'. gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Built target sak /usr/bin/gmake -f apps/sak/CMakeFiles/sak_doc.dir/build.make apps/sak/CMakeFiles/sak_doc.dir/depend gmake[4]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak/CMakeFiles/sak_doc.dir/DependInfo.cmake "--color=" gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/gmake -f apps/sak/CMakeFiles/sak_doc.dir/build.make apps/sak/CMakeFiles/sak_doc.dir/build gmake[4]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Generating README.sak.txt cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak && ../../bin/sak --export-help=txt > README.sak.txt [100%] Generating 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/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/sam2matrix /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/samcat /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/seqan_tcoffee /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/seqcons2 /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/sgip /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/snp_store /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/splazers /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/stellar /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/tree_recon /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/yara_indexer /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/yara_mapper + ln -s /usr/share/seqan2/pdf_plot_helper/plot.awk /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/plot.awk + ln -s /usr/share/seqan2/pdf_plot_helper/ps2pswLinks.gawk /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/bin/ps2pswLinks.gawk + rm -rf /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/libexec/seqan2/examples/ngs_roi/R + rm -f /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2/LICENSE + rm -f /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2/CHANGELOG.rst + rm -f /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2/README.rst + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.4.0-22.fc40 --unique-debug-suffix -2.4.0-22.fc40.s390x --unique-debug-src-base seqan2-2.4.0-22.fc40.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/seqan-seqan-v2.4.0 find-debuginfo: starting Extracting debug info from 44 files DWARF-compressing 44 files sepdebugcrcfix: Updated 44 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/seqan2-2.4.0-22.fc40.s390x 23498 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/bin/roi_plot_9.sh from /bin/bash to #!/usr/bin/bash mangling shebang in /usr/bin/roi_sort.sh from /bin/bash to #!/usr/bin/bash mangling shebang in /usr/bin/gff_sort.sh from /bin/bash to #!/usr/bin/bash mangling shebang in /usr/bin/bed_sort.sh from /bin/bash to #!/usr/bin/bash + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: seqan2-apps-2.4.0-22.fc40.s390x Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.hB8mE4 + umask 022 + cd /builddir/build/BUILD + cd seqan-seqan-v2.4.0 + DOCDIR=/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2-apps + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/README.rst /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/CHANGELOG.rst /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2-apps + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.svyHpe + umask 022 + cd /builddir/build/BUILD + cd seqan-seqan-v2.4.0 + LICENSEDIR=/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bs_tools-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_tools-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason2-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/ngs_roi-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/pair_align-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers3-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat/samcat-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/searchjoin-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons2-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon/tree_recon-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/yara-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema-COPYING /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-apps + RPM_EC=0 ++ jobs -p + exit 0 warning: absolute symlink: /usr/bin/plot.awk -> /usr/share/seqan2/pdf_plot_helper/plot.awk warning: absolute symlink: /usr/bin/ps2pswLinks.gawk -> /usr/share/seqan2/pdf_plot_helper/ps2pswLinks.gawk Provides: seqan = 0:2.4.0-22.fc40 seqan2-apps = 2.4.0-22.fc40 seqan2-apps(s390-64) = 2.4.0-22.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/bash libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(GOMP_4.5)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_2.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libm.so.6(GLIBC_2.4)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.11)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.2)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.10)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.17)(64bit) libstdc++.so.6(GLIBCXX_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.19)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.22)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libstdc++.so.6(GLIBCXX_LDBL_3.4.7)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Obsoletes: seqan <= 0:1.4.2 Processing files: seqan2-headers-2.4.0-22.fc40.s390x Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Ql30sn + umask 022 + cd /builddir/build/BUILD + cd seqan-seqan-v2.4.0 + DOCDIR=/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2-headers + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2-headers + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/README.rst /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2-headers + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/CHANGELOG.rst /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/doc/seqan2-headers + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.HCjdA5 + umask 022 + cd /builddir/build/BUILD + cd seqan-seqan-v2.4.0 + LICENSEDIR=/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-headers + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-headers + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x/usr/share/licenses/seqan2-headers + RPM_EC=0 ++ jobs -p + exit 0 Provides: bundled(bzip2stream) bundled(zipstream) cmake(seqan) pkgconfig(seqan-2) = 2.4.0 seqan2-headers = 2.4.0-22.fc40 seqan2-headers(s390-64) = 2.4.0-22.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/pkg-config cmake-filesystem(s390-64) pkgconfig(zlib) Processing files: seqan2-examples-2.4.0-22.fc40.s390x Provides: seqan2-examples = 2.4.0-22.fc40 seqan2-examples(s390-64) = 2.4.0-22.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: seqan2-debugsource-2.4.0-22.fc40.s390x Provides: seqan2-debugsource = 2.4.0-22.fc40 seqan2-debugsource(s390-64) = 2.4.0-22.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: seqan2-apps-debuginfo-2.4.0-22.fc40.s390x Provides: debuginfo(build-id) = 0253946c7f7b966a5bb62129061764f20a46bc91 debuginfo(build-id) = 0273189a22096e95f9ebaa7cf7bd06a679af1a57 debuginfo(build-id) = 067c88a5a18fce2e2042bd854323c011b1e21aaf debuginfo(build-id) = 0d02b8daf57a6c925864bad7114427d6e0cc65bf debuginfo(build-id) = 12f7456bbc2c489cd2b3efac07bcbc408ee0f27d debuginfo(build-id) = 179106f0a48b9afe8201d0cfda2a4b4924661f58 debuginfo(build-id) = 24ea5611a20cac7ff02039514a03ba531cb3278c debuginfo(build-id) = 2a9f8cd9d606e40dae09b4ad20d43b5e35c90d1e debuginfo(build-id) = 31eadae479b86bcb040330a3dc0fdba0041f554d debuginfo(build-id) = 3dad4ee95d7666118fd8e6b17e89ca29ace8e70d debuginfo(build-id) = 42d559eb6c55e1030bf876785492ef4dd5260290 debuginfo(build-id) = 436c46c6e98145baa81d292d8d17ed4f02157129 debuginfo(build-id) = 44e9c7b39c8963c5c93675e4afe83852c22e24d3 debuginfo(build-id) = 46da97e30f025717bf7cd862d2f8210fc779a0fa debuginfo(build-id) = 49b92165e9a92edc33211b5074c6c98093ee6314 debuginfo(build-id) = 4c5b60d30de981d7bda32cd86b4e885479fb608b debuginfo(build-id) = 5b83e5bdb1485a43f48e154ddb35d7827a3ca85f debuginfo(build-id) = 5f134163b5951239b1dee145c9a2d276f61b5bad debuginfo(build-id) = 60808a67e8bd06c109c8746f79119508203889f3 debuginfo(build-id) = 621dea02951c910551da132275589c80137c0532 debuginfo(build-id) = 7678ce1e0ab37850e24b1a85c90acb20fc6aa121 debuginfo(build-id) = 76aaecfc697e03767e79dccc65d19f31872b2d4d debuginfo(build-id) = 78d8946480a5277184d4683883b18d22cd2e1503 debuginfo(build-id) = 7c6d614303af3eb1821fb729b74239e04e87ff57 debuginfo(build-id) = 8127bbb57e413ed75446ff9e08560b23c7912482 debuginfo(build-id) = 81fe5422a459da323e0979e9d0b0399665332239 debuginfo(build-id) = 9918301ab29acb15002ace172ca6e8c08124bd9c debuginfo(build-id) = 9aa356a9df16e9fb8b4f5ccef644354597a443f1 debuginfo(build-id) = 9d59509c5d3f72111efab015051befce26b6689b debuginfo(build-id) = 9d8519d3efe93e3420f86a4282f3989fbf3bcf9d debuginfo(build-id) = a12a4fa36a84a2bfe785681ca430de3e82de31e2 debuginfo(build-id) = a73b6fe2f912e390fd81acb2e9cb573c7a536a3b debuginfo(build-id) = a962d389783f5c14e511e0bfb7f3bc4d64a24d29 debuginfo(build-id) = b06fe4fe6c8e082ab43e10808b24ff02eead08cb debuginfo(build-id) = c633eeef50564a195d48d72e780d2d58a44d80b0 debuginfo(build-id) = c7b4c7ade56376b5ae80170098f5a83856b024d6 debuginfo(build-id) = cefd1e98f08c4a6ac7ad2d142474bafc9921ec5e debuginfo(build-id) = d0f180c70212a48c0ba398df861edfe4df45cd77 debuginfo(build-id) = d8469b7d93a0452cbf22cd4802d64fb789a3cfee debuginfo(build-id) = e2aa50f2b26e47d2d2d60df82bc11a3392159c83 debuginfo(build-id) = ea5c096f7110302dc46bb8bd2843170e6b5204cc debuginfo(build-id) = ebda23c86c72c0ca618a196a48087aacf8c852ac debuginfo(build-id) = f069d2433758a65543d3d26f2182d9cb47a701a6 debuginfo(build-id) = fcd6f56ffbddb82ae741effaf023dafa46ee7f25 seqan2-apps-debuginfo = 2.4.0-22.fc40 seqan2-apps-debuginfo(s390-64) = 2.4.0-22.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: seqan2-debugsource(s390-64) = 2.4.0-22.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x Wrote: /builddir/build/RPMS/seqan2-apps-2.4.0-22.fc40.s390x.rpm Wrote: /builddir/build/RPMS/seqan2-headers-2.4.0-22.fc40.s390x.rpm Wrote: /builddir/build/RPMS/seqan2-debugsource-2.4.0-22.fc40.s390x.rpm Wrote: /builddir/build/RPMS/seqan2-examples-2.4.0-22.fc40.s390x.rpm Wrote: /builddir/build/RPMS/seqan2-apps-debuginfo-2.4.0-22.fc40.s390x.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.QTg8jJ + umask 022 + cd /builddir/build/BUILD + cd seqan-seqan-v2.4.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.s390x + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.rBp7wf + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/seqan-seqan-v2.4.0-SPECPARTS + rm -rf seqan-seqan-v2.4.0 seqan-seqan-v2.4.0.gemspec + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: absolute symlink: /usr/bin/plot.awk -> /usr/share/seqan2/pdf_plot_helper/plot.awk absolute symlink: /usr/bin/ps2pswLinks.gawk -> /usr/share/seqan2/pdf_plot_helper/ps2pswLinks.gawk Finish: rpmbuild seqan2-2.4.0-22.fc40.src.rpm Finish: build phase for seqan2-2.4.0-22.fc40.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-s390x-1706587007.973351/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-s390x-1706587007.973351/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-s390x-1706587007.973351/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/seqan2-2.4.0-22.fc40.src.rpm) Config(child) 69 minutes 36 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "seqan2-apps-debuginfo", "epoch": null, "version": "2.4.0", "release": "22.fc40", "arch": "s390x" }, { "name": "seqan2-headers", "epoch": null, "version": "2.4.0", "release": "22.fc40", "arch": "s390x" }, { "name": "seqan2-apps", "epoch": null, "version": "2.4.0", "release": "22.fc40", "arch": "s390x" }, { "name": "seqan2", "epoch": null, "version": "2.4.0", "release": "22.fc40", "arch": "src" }, { "name": "seqan2-examples", "epoch": null, "version": "2.4.0", "release": "22.fc40", "arch": "s390x" }, { "name": "seqan2-debugsource", "epoch": null, "version": "2.4.0", "release": "22.fc40", "arch": "s390x" } ] } RPMResults finished